Packages for the base R system have been part of the Debian distribution since 1997, thanks to Douglas Bates, and are diligently maintained by Dirk Eddelbuettel since 2001. R, as well as many add-on packages (from CRAN and others repositories) are available via the regular Debian distribution mechanisms. Hence, running
apt-cache search "^r-.*" | sortin a shell should get you started with a list of available packages. Don’t forget to add sudo to commands that need writing privileges and you are not running them as the root user.
The latest stable version of R and many R packages from CRAN and the Bioconductor project are readily available in official Debian sid repositories.
With an appropriate entry in /etc/apt/sources.list (see below for Debian branches other than sid/unstable), the newest R release including recommended packages can be installed using a command sequence like
apt-get update
apt-get install r-base r-base-devWhile updating your package lists you might get a warning about a missing key, telling you that the integrity of packages can not be verified. You can ignore this if you trust the CRAN servers and continue with the installation. Otherwise, please refer to the section on secure apt below.
You only need r-base-dev if you want to compile R packages yourself or other software depending on R (see section below on administration and maintenance). Be aware that you may also have to install build dependencies (typically -dev packages containing headers). The list r-sig-debian is a good place to ask if you run into problems.
You may want to install the automatically tuned Atlas or the multi-threaded OpenBlas library in order to get higher performance for linear algebra operations
apt-get install libatlas3-baseor
apt-get install libopenblas-baseThe R packages part of r-base and r-recommended are installed into the directory /usr/lib/R/library. The other R packages available as precompiled Debian packages r-cran-* and r-bioc-* are installed into /usr/lib/R/site-library.
These can be updated using usual Debian package maintenance tools like apt-get or aptitude.
The command
apt-cache rdepends r-base-coreshows all packages that depend on r-base-core. This comprises a large number of contributed packages from CRAN and other repositories.
If you want to install R packages not provided as Debian packages, or if you want to use newer versions, you need to build them from source which requires the development package r-base-dev that can be installed by
apt-get install r-base-devThis pulls in the basic requirements for compiling R packages. R packages may then be installed by the local user/admin from the CRAN source packages, typically from inside R using the
R> install.packages()function or using
R CMD INSTALLfrom a shell. If you have proper write permissions in /usr/local/lib/R/site-library/, and you have not set R_LIBS_USER manually, they will be installed there. Otherwise, you will be asked if a directory in your home directory should be created for these packages. A routine update of such locally compiled packages can be done using
R> update.packages(.libPaths()[1])which will update the packages in the first part of your library path. You can have a look at the components of this path by
R> .libPaths()If you would like to update R packages that have been installed via the Debian package management system which are installed somewhere under /usr/lib/, I would recommend to do this the Debian way using the source packages from Debian unstable.
In order to find packages, R looks at the variables R_LIBS_USER and R_LIBS_SITE. On Debian and Ubuntu, R_LIBS_USER is set in /etc/R/Renviron to
R_LIBS_USER=${R_LIBS_USER-'~/R/$platform-library/4.0'}where $platform is something like 'x86_64-pc-linux-gnu' and depending on the version of R installed. You can override this in ~/.Renviron. R_LIBS_SITE is set in /etc/R/Renviron to
R_LIBS_SITE=${R_LIBS_SITE-'/usr/local/lib/R/site-library:/usr/lib/R/site-library:/usr/lib/R/library'}This means that packages installed from within R take precedence over the ones installed via the Debian package management system if you happen to have two versions installed at the same time.
As R and related packages are currently not part of the official Debian backports repositories like buster-backports (please contact r-sig-debian if you would like to change this), the R versions in released or frozen Debian releases get out of date. Therefore, updates of a subset of these R related packages are provided here for such Debian releases.
The packages recommended by the R core team (r-recommended) are updated in the Debian repositories on CRAN upon each new release of R (at least for the main architectures amd64 and i386). These packages are:
r-cran-boot
r-cran-class
r-cran-cluster
r-cran-codetools
r-cran-foreign
r-cran-kernsmooth
r-cran-lattice
r-cran-mass
r-cran-matrix
r-cran-mgcv
r-cran-nlme
r-cran-nnet
r-cran-rpart
r-cran-spatial
r-cran-survivalBackports of the following packages are also supplied and kept up to date in the same manner:
littler
rpy2
rkwardAny help is welcome in case you would like to see additional packages here.
Since 16th of November 2021, the bullseye-cran40, buster-cran40, and since 17th of November also the buster-cran35 and stretch-cran35 repositories are signed with a new key with key ID 0xB8F25A8A73EACF41, key fingerprint 95C0FAF38DB3CCAD0C080A7BDC78B2DDEABC47B7 and user ID Johannes Ranke <johannes.ranke@jrwb.de>.
You can fetch and import the current key using
apt-key adv --keyserver keyserver.ubuntu.com --recv-key '95C0FAF38DB3CCAD0C080A7BDC78B2DDEABC47B7'Note that you need to add sudo if you are not running this as root. In case you are behind a firewall blocking port 11371, you can specify a proxy server by adding --keyserver-options http-proxy=<PROXY> in the above command.
Debian bullseye has been released with R 4.0.4. If you want to upgrade to R 4.2.1 on bullseye, you can use the following repository.
deb http://cloud.r-project.org/bin/linux/debian bullseye-cran40/Note that R 4.1.x, and again R 4.2.x have bumped the Graphics API, so graphics packages like svglite, tikzDevice, rgl, rvg, ggplot2 or vdiffr (embedding svglite) will need to be reinstalled. This also affects the graphics device supplied by rkward. If you don’t you will get an error message
Graphics API version mismatchFor a backport of R 4.2.1 to buster, please add
deb http://cloud.r-project.org/bin/linux/debian buster-cran40/to the file /etc/apt/sources.list on your computer.
Due to the API change (R 4.0.x and 4.1.0 provide r-api-4), installing R 4.x.x will remove all Debian packages dependent on r-api-35, with the exception of the ones provided here. Also, you will need to update R packages that you have obtained directly from CRAN or Bioconductor.
You can install using
apt update
apt install -t buster-cran40 r-basePlease refer to the note above on the Graphics API version bump.
In addition, if you had a large number of locally installed packages before the change to r-api-4, updating them using e.g. the command given below may take some time, also depending on the number of CPU threads you run in parallel:
update.packages(lib.loc="/usr/local/lib/R/site-library", ask = FALSE,
checkBuilt = TRUE, Ncpus = 16)In my case, using 16 parallel threads as specified in the command above, the downloading took about eight minutes and the first round of installation with heavy CPU load took another 12 minutes. Then it stopped mentioning that I needed to manually reinstall testthat, which I did using install.packages(). This may be necessary due to a circular dependency, as Dirk pointed out in his upgrade report on his blog. After I did that, I ran the update command again and it took another six minutes until it successfully completed.
If you have Bioconductor packages installed as well, you need to switch to the current version using the commands listed here.
A backport of R 3.6.3 to buster is also available, which does not require reinstalling extension packages.
deb http://cloud.r-project.org/bin/linux/debian buster-cran35/For a backport of R 3.6.3 to stretch, please add
deb http://cloud.r-project.org/bin/linux/debian stretch-cran35/to the file /etc/apt/sources.list on your computer.
Please note that R packages from the Debian stretch distribution are not compatible with R 3.5.x, as it provides r-api-3.5, while the stretch packages depend on r-api-3.
Also, local packages installed before the update to R 3.5.0 will not work correctly if they use compiled code.
R packages you have compiled locally can be updated using
update.packages(lib.loc="/usr/local/lib/R/site-library", ask=FALSE, checkBuilt=TRUE)There is also an old repository containing R 3.4.4 that still has arm64 and armhf binaries:
deb http://cloud.r-project.org/bin/linux/debian stretch-cran34/The last R release backported to jessie and made available on CRAN is currently R 3.5.3. For a backport of R 3.5.3 to jessie, please add
deb http://cloud.r-project.org/bin/linux/debian jessie-cran35/to the file /etc/apt/sources.list on your computer.
For jessie, the same notes given in the section for stretch apply, i.e. packages from the Debian archive are not compatible with this backport, and locally compiled packages may have to be rebuilt.
The last R release backported to wheezy and made available on CRAN is currently R 3.2.5 with the codename “Very, Very Secure Dishes”.
In order to address the security vulnerability https://security-tracker.debian.org/tracker/CVE-2016-8714, I applied the commits r71664 and r71667 to src/library/grDevices/src/devPS.c.
Backporting R 3.3.0 and later would entail backporting curl 7.28 to wheezy, which in turn would require libgnutla28-dev (which is available in wheezy-backports), linghttp2-dev (only available in jessie) and librtmp-dev >= 2.4+20131018.git (not available in wheezy).
The milestone release R 3.0.0 published on April 3, 2013 is not compatible with any R packages built on earlier versions. This means that R packages from the Debian wheezy archive do not work under R 3.x.y. This is the source line needed for R 3.x.y on Debian wheezy
deb cloud.r-project.org/bin/linux/debian wheezy-cran3/Of course the R packages r-cran-* provided here are compiled using the current R version. Before installing R 3.x.y be sure you do not rely on loading R packages from Debian wheezy. If unsure, look at the debs you have installed using
dpkg --get-selections | grep r-cranand compare with the list of packages supported here (see above, also for a procedure to upgrade packages install locally from source R packages).
This repository also contains backports of tcl8.6, tk8.6 and texinfo for wheezy, as the upstream Debian package of R >= 3.2.0 need these versions.
Please be aware that the R packages available as binary .deb packages in wheezy (with names starting with r-cran-) are not compatible with R versions 3.0.0 and later. Only a confined number of R packages is provided here.
Updating packages installed locally from sources, which you need to do after an upgrade from R 2.a.b to R 3.x.y, is explained below under the section administration and maintenance. What you probably need to do is
R> update.packages(.libPaths()[1], checkBuilt=TRUE)in R in order to rebuild packages that are installed in addition to the Debian r-cran-* packages. For other changes in R please refer to the NEWS file.
There are i386 and amd64 binaries for wheezy and later releases. Since R 3.1.0, R is fully functional on arm and armel binaries for jessie and wheezy were provided here up to R 3.4.2. Since R 3.4.2 and up to R 3.4.4, binaries for armhf and arm64 were provided for Debian stretch (with the exception of R 3.4.3 on arm64, see this bug).
For other architectures and releases, you can use the source packages from one of these repositories
deb-src cloud.r-project.org/bin/linux/debian bullseye-cran40/
deb-src cloud.r-project.org/bin/linux/debian buster-cran40/
deb-src cloud.r-project.org/bin/linux/debian buster-cran35/
deb-src cloud.r-project.org/bin/linux/debian stretch-cran35/
deb-src cloud.r-project.org/bin/linux/debian jessie-cran35/to compile binary Debian packages.
The best place to report problems with these packages or ask R questions specific to Debian is the r-sig-debian mailing list. See
https://stat.ethz.ch/mailman/listinfo/r-sig-debian
for more information.
Anyone interested in building Debian packages (e.g. for an unsupported release, another architecture or an old R version) can have a look at the build scripts used by the current maintainer. These can be inspected at
http://cgit.jrwb.de/r-backports
or cloned from the git repository
git clone http://cgit.jrwb.de/r-backportsThe scripts contain some small changes needed to compile the original Debian packages on the supported release.
The following notes are an attempt to merge the hints given in a thread on r-sig-debian started end of March 2015, and the tips given at https://developer.r-project.org/SVNtips.html. I have not used this a lot and I assume you have some experience in building software on unix systems. No warranties, your mileage may vary.
First, make sure you have a source repository in your /etc/apt/sources/list, like
deb-src cloud.r-project.org/bin/linux/debian stretch-cran35/in order to make it easier to get the build dependencies. Then update your list of available packages and run as root
apt-get build-dep r-baseTo install the build dependencies. The following commands do not need root privileges, and are safer to run as a normal user.
I keep all sources managed by subversion under ~/svn, so I do
export RTOP=~/svn/RPlease adapt to your needs. The location of the source code for the base R system is conveniently defined as en environment variable by
export REPOS=https://svn.r-project.org/RWe change to our RTOP directory and check out the latest revision of R-devel
cd $RTOP
svn co $REPOS/trunk r-devel/source
mkdir $RTOP/r-devel/buildThe second time around we only need to
cd $RTOP/r-devel/source
svn upThen we need to get the sources of the recommended packages
cd $RTOP/r-devel/source/tools
./rsync-recommendedWe build in the separate directory created above, in order not to pollute the source code
cd $RTOP/r-devel/build
../source/configureThere are a lot of configure options you might want to use, for example you will probably want --with-blas="-lopenblas" to get more performant linear algebra operations. This depends on libopenblas-dev to be installed, which, per default, will pull libopenblas-pthread-dev on Debian bullseye.
We are not using the install target here, so we do not set --prefix. This is to avoid conflicts with the Debian packages of released versions of R. The next step builds the sources.
make
make check
make pdf
make infoOf course doing checks and making pdf and info documentation is optional. Then we use links to make R-devel and Rscript-devel available (obviously supposes write permission on /usr/local/bin).
cd /usr/local/bin
ln -s /$RTOP/r-devel/build/bin/R R-devel
ln -s /$RTOP/r-devel/build/bin/Rscript Rscript-develThis will make the commands R-devel and Rscript-devel available. Note that the only entry on .libPaths() is $RTOP/r-devel/build/library, so this is where packages will be installed.
After the release of a version R-x.y.0, the so-called release branch is used to introduce changes that meet the development guidelines.
We can build such branches (aka R-patched) using the following scheme, which is adapted from the procedure given for R-devel, but without duplicating all comments.
At the time of this writing, the release branch can be defined by
export RPATCHED=branches/R-3-5-branchR-patched can than be built and made available by
cd $RTOP
svn co $REPOS/$RPATCHED r-patched/source
mkdir $RTOP/r-patched/build
cd $RTOP/r-patched/source/tools
./rsync-recommendedAgain, we build in the separate directory created above, in order not to pollute the source code
cd $RTOP/r-patched/build
../source/configure
make
make check
make pdf
make infoThen, as privileged user:
cd /usr/local/bin
ln -s /$RTOP/r-patched/build/bin/R R-patched
ln -s /$RTOP/r-patched/build/bin/Rscript Rscript-patchedThe builds can be updated by updating the sources from the repository, syncing the latest versions of the recommended packages and rebuilding.
An RFC on a first public draft of ‘Debian R Policy’ has been posted to debian-devel in 2003.
The Debian R packages are maintained by Dirk Eddelbuettel. The packages present on CRAN for Debian stable and oldstable are provided by Johannes Ranke. Thanks to Mathieu Basille for restructuring the README in March 2015.