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
--
Dr. Michael A. Rutter
School of Science
Penn State Erie, The Behrend College
Station Road
Erie, PA 16563
http://math.bd.psu.edu/faculty/rutter
On Fri, Apr 27, 2012 at 8:11 PM, Michael Rutter <mar36 at psu.edu> wrote:> If you want additional packages (over 1,100), you can check out my > cran2deb4ubuntu PPA: > > https://launchpad.net/~marutter/+archive/c2d4u >Very interesting! Thanks for sharing this with us. It looks like 'cran2deb' did evolve to a useful state.> 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. >Is there a reason to limit 'cran2deb4ubuntu' to Task Views packages? For example, I would like to install all the Rcmdr plug-ins via the PPA but the only one available is 'rcmdrplugin.doe'. Very useful GUIs such as 'playwith' and 'latticist' are missing, too. Even some popular toolkit deps are missing: 'gwidgetstcltk'. Are there plans to increase the number of packages provided? Regards Liviu
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
On 04/30/2012 01:54 AM, Liviu Andronic wrote:> On Mon, Apr 30, 2012 at 2:04 AM, Michael Rutter<mar36 at psu.edu> wrote: >> I had to draw a line somewhere. Maintaining all the packages was out of the >> question, as the number is just too high. Since there is no list at this >> time of the most popular packages, I choose the Task View lists as a good >> place to start. If and when this number of packages becomes manageable, I >> may add more. >> > I see, thanks for letting me know. Although not as reliable as the > Task Views, could the Crantastic popularity contest [1] be used for > this purpose? > > Regards > LiviuThat is a possibility. Once I get all the bugs worked out, it will be something to consider. Michael -- Dr. Michael A. Rutter School of Science Penn State Erie, The Behrend College Station Road Erie, PA 16563 http://math.bd.psu.edu/faculty/rutter