r2u: CRAN as Ubuntu Binaries
Full integration with
aptas every binary resolves all its dependencies: No more installations (of pre-built archives) only to discover that a shared library is missing. No more surprises.
Full integration with
aptso that an update of a system library cannot break an R package: if a (shared) library is used by a CRAN, the package manager knows and will not remove it. No more (R package) breakage from (system) library updates.
Installations are fast, automated and reversible thanks to package management layer.
Complete coverage with (currently) ~ 19,700 CRAN packages (and 230+ from BioConductor).
Complete support for both Ubuntu 20.04 ("focal") and Ubuntu 22.04 ("jammy").
Optional (but recommeded) bspm use automagically connects R functions like
aptfor access to binaries and dependencies.
The gif below shows how one
install.packages("tidyverse") command on an Ubuntu
20.04 system installs all packages and dependencies as binaries in 18 seconds (by passing the
R package installation to
apt using bspm).
This uses the Docker container referenced below, which has been set up with the five easy setup steps detailed here.
What is Covered ?
We generally support amd64 (i.e. standard Intel/AMD cpus) for the Ubuntu LTS release and the predecessor release. We use 'r-release' just like CRAN. So currently the 'focal' 20.04 LTS and 'jammy' 22.04 LTS releases are fully supported.
Support for other cpu architectures is certainly possible but somewhat unlikely due to a lack of (additional hardware) resources and time. Support for other distributions is possible but unlikely right now (due to a lack of resources and time). We hope to cover Debian at some point.
Current versions are R 4.2.1, and BioConductor release 3.15 packages are provided when required by CRAN packages.
What is Selected ?
Initially, we started from cran-logs by picking the N most-downloaded packages, along with their dependencies from BioConductor. (It should be noted that for example the first 100 packages already account for approximately half the total downloads: it is a very skewed distribution.) We iterated, and fairly soon arrived of full coverage of CRAN.
So we now cover
- all CRAN packages (modulo at best handful of blacklisted ones) including all packages needing compilation
- all BioConductor package that are implied by these (and build for us).
This currently resuls in 19772 and 19667 binary packages from CRAN in "focal" and "jammy", respectively, and 230 and 235 BioConductor packages, respectively, from the 3.15 release.
The sole exception are two packages we cannot build (as we do not have the required commercial software it accessess) plus less than a handful of 'odd build' that fail.
What is it Based On?
For the CRAN binaries we either repackage RSPM builds (where available) or build natively. All selected BioConductor 3.15 packages are built natively. For all of these, full dependency resolution and integration with the system is a key feature.
Everything is provided as
.deb binary files with proper dependency
resolution by using a proper
apt repo which also has a signed Release file.
Usage and Setup
First add the repository key so that
apt knows it (this is optional but recommended)
apt install --yes --no-install-recommends wget # to add the key wget -q -O- https://eddelbuettel.github.io/r2u/assets/dirk_eddelbuettel_key.asc \ | tee -a /etc/apt/trusted.gpg.d/cranapt_key.asc
Second, add the repository to the
apt registry. You can use the original host
echo "deb [arch=amd64] https://dirk.eddelbuettel.com/cranapt focal main" \ > /etc/apt/sources.list.d/cranapt.list apt update
or use the mirror at the University of Illinois Urbana-Champaign:
echo "deb [arch=amd64] https://r2u.stat.illinois.edu/ubuntu focal main" \ > /etc/apt/sources.list.d/cranapt.list apt update
(In either example, replace
jammy for use with Ubuntu 22.04.)
Third, and optionally, if you do not yet have the current R version, run these two lines (or use the standard CRAN repo setup)
wget -q -O- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc \ | tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc echo "deb [arch=amd64] https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/" \ > /etc/apt/sources.list.d/cran-ubuntu.list
jammy for use with Ubuntu 22.04.)
Fourth, add repository 'pinning' as
apt might get confused by some older
packages (in the Ubuntu distro) which accidentally appear with a higher
version number. See the next section to ensure 'CRANapt' sorts highest.
After that the package are known (under their
names). You can install them on the command-line using
aptitude as well as other front-ends.
Fifth, and also optional, install and enable the
bspm package so that CRANapt and
other packages become available via
update.packages(). Note that you may need to install it directly from source via
sudo Rscript -e
'install.packages("bspm")' to ensure it integrates correctly with the packaging system.
Because we let
apt (and related tools) pick the packages, we have to ensure
that the CRANapt repo sorts higher than the default repo as (older)
package builds in the distribution itself may appear (to
apt) to be
newer. A case in point was package
gtable whose version in Ubuntu was
0.3.0+dfsg-1 which accidentally sorts higher than the rebuild we made under
a newer and more consistent version number
0.3.0-1.ca2004.1. One possible
fix is 'apt pinning'. Place a file
/etc/apt/preferences.d/99cranapt with content
Package: * Pin: release o=CRAN-Apt Project Pin: release l=CRAN-Apt Packages Pin-Priority: 700
which will now give packages from this repo a higher default priority of 700 overriding the standard value of 500.
Note that with recent builds of Docker (and possibly related to Ubuntu hosts) you may have to add
--security-opt seccomp=unconfined option to your Docker invocation to take advantage of bspm
and the full system integration inside the container.
This is also documented in the FAQ.
We also found that when building containers based off the
r2u containers, we could not rely on the
bspm integration as it requires superuser rights to pass off commands from
You can still use
r2u containers as a base, but sadly have to turn off
bspm and use just
commands to install packages.
Use this link below (after possibly signing up for gitpod.io first)
and run one of the three example scripts, or just start R in the terminal window.
Please file issues at the GitHub issues for r2u.
The littler package reflects build-time configuration, the RSPM binary is then expecting a different R location so it needs a binary rebuild. Added a 'force' flag, may need a list similar to the blacklist to always compiled.
A small number of packages do not build for lack required components; examples are ROracle and Rcplex. They, and their reverse dependencies, are are blacklisted and not built.
r2u is an
aptrepo, which via
bspmbecomes used "automagically" via standard R calls of
install.packages()and alike. That last part is important: package installations that do not use
install.packages()(such as the RStudio GUI,
rig, ...) do not benefit from
aptfor you, and cannot take advantage of r2u.
[DONE] In May, some geospatial packages do not currently install on 20.04, adding the UbuntuGIS PPA as a base may help. This is not an issue on 22.04. It also no longer appears to be an issue with 20.04 now.
[DONE] The BioConductor release is still at 3.14 and should be upgraded to the now-current 3.15.
[DONE] Support for Ubuntu 22.04 has been added as well.
[DONE] Package nlme needed special treatment because the Debian/Ubuntu binary changed the 'hyphenated' version to a 'dot-separated' one leading to an inverted sorting order (see issue #7, as well as the FAQ, for more on this).
[DONE] Because Java is so special (and keeps its libraries 'elsewhere', the shared library dependence for package rJava was not fully specified. We added a special treatment for it.
terraneeded a dependency adjustment on 'focal' for their most recent versions.
The repository-building code in this package is released under the GPL (>= 2).
All CRAN and BioConductor packages are released under their respective licenses.
This was made possible by the generous support of endless coffee thanks to my GitHub Sponsors.