UBUNTU PACKAGES FOR R

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R packages for Ubuntu on i386 and amd64 are available for all stable Desktop releases of Ubuntu until their official end of life date. However, only the latest Long Term Support (LTS) release is fully supported.  As of May 5, 2015 the supported releases are Vivid Vervet (15.04), Trusty Tahr (14.04; LTS), and Precise Pangolin (12.04; LTS)

See https://wiki.ubuntu.com/Releases for details.

# Installation

To obtain the latest R packages, add an entry like

    deb https://<my.favorite.cran.mirror>/bin/linux/ubuntu vivid/

or

    deb https://<my.favorite.cran.mirror>/bin/linux/ubuntu trusty/
   
or

    deb https://<my.favorite.cran.mirror>/bin/linux/ubuntu precise/
   
or

in your /etc/apt/sources.list file, replacing <my.favorite.cran.mirror> by the actual URL of your favorite CRAN mirror. See https://cran.r-project.org/mirrors.html for the list of CRAN mirrors. To install the complete R system, use

    sudo apt-get update
    sudo apt-get install r-base

Users who need to compile R packages from source [e.g. package maintainers, or anyone installing packages with install.packages()] should also install the r-base-dev package:

    sudo apt-get install r-base-dev

The R packages for Ubuntu otherwise behave like the Debian ones. One may find additional information in the Debian README file located at https://cran.R-project.org/bin/linux/debian/.

Installation and compilation of R or some of its packages may require Ubuntu packages from the "backports" repositories. Therefore, it is suggested to activate the backports repositories with an entry like 

    deb https://<my.favorite.ubuntu.mirror>/ trsuty-backports main restricted universe

in your /etc/apt/sources.list file. See https://launchpad.net/ubuntu/+archivemirrors for the list of Ubuntu mirrors.


# Supported Packages

A number of R packages are available from the Ubuntu repositories with names starting with r-cran-. The following ones are kept up-to-date on CRAN: all packages part of the r-recommended bundle, namely

- 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-survival

as well as

- r-cran-rodbc

The other r-cran-* packages are updated with Ubuntu releases only. Users who need to update one of these R packages (say r-cran-foo) should first make sure to obtain all the required build
dependencies with

    sudo apt-get build-dep r-cran-foo

Because they rely on the installed version of R, we also provide, on an experimental basis, versions of the following packages as up-to-date as the Ubuntu release allows:

- littler
- python-rpy
- python-rpy-doc
- python-rpy2

Please notice that the maintainers are not necessarily themselves users of these packages, so positive or negative feedback through the usual channels (see below) would be appreciated.

Finally, as an added convenience to Ubuntu users who interact with R through Emacs, we also provide an up-to-date version of the package

- ess


# Secure APT

The Ubuntu archives on CRAN are signed with the key of "Michael Rutter <marutter@gmail.com>" with key ID E084DAB9.  To add the key to your system with one command use (thanks to Brett Presnell for the tip):

    sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9

An alternate method can be used by retrieving the key with

    gpg --keyserver keyserver.ubuntu.com --recv-key E084DAB9

and then feed it to apt-key with

    gpg -a --export E084DAB9 | sudo apt-key add -

Some people have reported difficulties using this approach. The issue is usually related to a firewall blocking port 11371. If the first gpg command fails, you may want to try (thanks to Mischan Toosarani for the tip):

    gpg --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys E084DAB9

and then feed it to apt-key with

    gpg -a --export E084DAB9 | sudo apt-key add -

Another alternative approach is to search for the key at https://keyserver.ubuntu.com:11371/ and copy the key to a plain text file, say key.txt. Then, feed the key to apt-key with

    sudo apt-key add key.txt


# Administration and Maintances of R Packages

The R packages part of the Ubuntu r-base and r-recommended packages are installed into the directory /usr/lib/R/library. These can be updated using apt-get with

    sudo apt-get update
    sudo apt-get upgrade

The other r-cran-* packages shipped with Ubuntu are installed into the directory /usr/lib/R/site-library.

Installing R packages not provided with Ubuntu first requires tools to compile the packages from source. These tools are installed via the R development package with

    sudo apt-get install r-base-dev

Then a site administrator can install R packages into the directory /usr/local/lib/R/site-library by running R as root and using the 

    > install.packages()

function. A routine update can then be undertaken from R using

    > update.packages(lib.loc = "/usr/local/lib/R/site-library")

The paths above are stored in the R_LIBS_SITE environment variable defined in the /etc/R/Renviron file.

Individual users can install R packages into their home directory. The simplest procedure is to create a file ~/.Renviron containing, e.g.,

    R_LIBS_USER="~/lib/R/library"

The install.packages() and update.packages() functions will then work in directory ~/lib/R/library. It is also possible to automatically create version-specific library trees; see ?.libPaths in R for more information.


# Reporting Problems

The best place to report problems with these packages or ask R questions specific to Ubuntu is the R-SIG-Debian mailing list. See

  https://stat.ethz.ch/mailman/listinfo/r-sig-debian

for more information.


# Acknowledgements

The Debian R packages are maintained by Dirk Eddelbuettel. The Ubuntu packages are compiled for i386 and amd64 by Michael Rutter using scripts developed by Vincent Goulet.