On 04/27/2012 02:11 PM, Michael Rutter wrote:
As per a request, here is a brief guide to what is available to R
users as packages in Ubuntu.
Each release of Ubuntu includes the latest version of R and the
recommended packages. In addition, there are approximately 80
additional r-cran packages available in the default repositories. The
limitation to these packages is that they are not updated and reflect
the current version of the program or package when that version of
Ubuntu was released.
If you want to have current versions of R and the recommended
packages, there are two repositories to choose from:
CRAN: http://cran.r-project.org/bin/linux/ubuntu/
Launchpad PPA: https://launchpad.net/~marutter/+archive/rrutter
Both sites have the same packages (the PPA packages are mirrored on
CRAN), but there may be a reason to use one over the other.
CRAN Advantages:
- A local mirror may be faster in terms of internet speed.
- Older versions of the packages are available, so if an update to R
or a core package breaks your code, you can reinstall an older version
via synaptic or apt.
PPA Advantages:
- Quickest way to get the updates (only by about 24 hours however)
- Easy to install (sudo add-apt-repository ppa:marutter/rrutter)
If you have been using CRAN, then there is no reason to change to the
PPA, as the same packages is provided at both locations. I will
continue to maintain both sites, so no need to worry about one or the
other going away.
If you want additional packages (over 1,100), you can check out my
cran2deb4ubuntu PPA:
https://launchpad.net/~marutter/+archive/c2d4u
In theory, this PPA has all the packages listed in the CRAN Task Views
and any dependencies. In practice, is has about 98% of them, as some
packages have issues. These packages can be installed via synaptic or
apt (sudo apt-get install r-cran-ggplot2, for example). The main
advantage of this approach is that tricky Ubuntu package requirements
will automatically be installed when installing the package. They
will also be automatically updated during normal Ubuntu updates, which
is another advantage. These packages are NOT installed when a
install.packages("foo") command is used from within R.
One of my plans this summer/sabbatical is create documentation for the
cran2deb4ubuntu project and give more information about what is and
what is not available.
If you have any further questions, please let me know.
Michael
Michael,
Thanks so much for this information. I have a question about
cran2deb4ubuntu PPA. Currently I use a CRAN repository, then
install.packages() within R for whatever isn't available in the
repository. If I want to use cran2deb4ubuntu, does it completely replace
the CRAN repository? Or do I use both and let the package manager
determine where to retrieve a package from?
Also, since I have many packages installed within R, do you know what
the effect would be of adding the PPA? Would installed packages get
updated, or would I have to uninstall in R and reinstall via PPA?
Thanks again for your work on this.
--Lee
--
Lee Hachadoorian
PhD, Earth& Environmental Sciences (Geography)
Research Associate, CUNY Center for Urban Research
http://freecity.commons.gc.cuny.edu
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