update R on ubuntu

vi /etc/apt/sources.list

http://cran.r-project.org/bin/linux/ubuntu/

deb http://cran.r-project.org/bin/linux/ubuntu lucid/

&UBUNTU PACKAGES FOR R Announcement: Due to sever issues, the Ubuntu CRAN packages have been signed with a new pgp key. See SECURE APT below. 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 April 28, 2011, the supported releases are Quantal Quetzal (12.10), Precise Pangolin (12.04; LTS), Oneiric Ocelot (11.10), Natty Nawwhal (11.04), Lucid Lynx (10.04; LTS) and Hardy Heron (8.04; LTS). See https://wiki.ubuntu.com/Releases for details. The previous LTS release, Hardy Heron (8.04), will remain supported as long as backporting of packages does not involve too much additional work (as is currently the case). INSTALLATION To obtain the latest R packages, add an entry like deb http://<my.favorite.cran.mirror>/bin/linux/ubuntu quantal/ or deb http://<my.favorite.cran.mirror>/bin/linux/ubuntu precise/ or deb http://<my.favorite.cran.mirror>/bin/linux/ubuntu oneiric/ or deb http://<my.favorite.cran.mirror>/bin/linux/ubuntu natty/ or deb http://<my.favorite.cran.mirror>/bin/linux/ubuntu lucid/ or deb http://<my.favorite.cran.mirror>/bin/linux/ubuntu hardy/ in your /etc/apt/sources.list file, replacing <my.favorite.cran.mirror> by the actual URL of your favorite CRAN mirror. See http://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 http://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. In particular, this is the case for Tcl/Tk 8.5 on Hardy. Therefore, it is suggested to activate the backports repositories with an entry like deb http://<my.favorite.ubuntu.mirror>/ precise-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 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 <[email protected]>" 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 retriving 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 http://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 MAINTENANCE 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. ACKNOWLEDGEMENT 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.