[Bio-Linux] [Fwd: [R-sig-Debian] Moving to R 3.0.0 on Ubuntu]
Tim Booth
tbooth at ceh.ac.uk
Thu Mar 28 05:42:26 EDT 2013
Dear Bio-Linux Users,
The message below is relevant to anyone who uses R. The basic gist is
that you have until 1st May to decide if you want to upgrade to the
latest R 3.0.0 or stay with R 2.15 on your system for now. You will
have to take some action either way. I'll prepare some specific
instructions for Bio-Linux users when Michael releases more info but you
should start to think about this now.
This page lists the changes in version 3.0.0:
http://stat.ethz.ch/R-manual/R-devel/doc/html/NEWS.html
If you do not use R, or if you only use R as part of a larger package
like Galaxy, this change will hopefully not trouble you. I will do some
testing here to ensure there are no unexpected knock-on effects from the
upgrade for non R users.
Cheers,
TIM
-------- Forwarded Message --------
From: Michael Rutter <mar36 at psu.edu>
Reply-to: "mar36 at psu.edu" <mar36 at psu.edu>
To: r-sig-debian at r-project.org <r-sig-debian at r-project.org>
Subject: [R-sig-Debian] Moving to R 3.0.0 on Ubuntu
Date: Wed, 27 Mar 2013 20:08:16 +0000
This is a post I just added to my Ubuntu R Blog
(http://www.personal.psu.edu/mar36/blogs/the_ubuntu_r_blog/2013/03/moving-to-r-300-on-ubuntu.html).
As you may (or may not) be aware of, R 3.0.0 is [scheduled to be
released](http://www.r-project.org/) on April 3rd. Since this is a
major release and there may be some growing pains (but I hope not) in
the move 3.0.0, here is some information about how I will handle R 3.0.0
on CRAN and my PPAs for Ubuntu.
**All packages must be rebuilt for R 3.0.0**
Any installed packages you are currently using will have to be rebuilt
using R 3.0.0. This could lead to some issues, especially is you are
using the Ubuntu binaries on CRAN or my PPA. I will try to minimize
these issues.
**CRAN and RRutter PPA are now frozen to R 2.15.3 (with one exception)**
Since many users would probably be alarmed to have production machines
upgrade to R 3.0.0 without testing to see if any thing breaks, the
packages on [CRAN](http://cran.us.r-project.org/bin/linux/ubuntu/) and
the [RRutter PPA](https://launchpad.net/~marutter/+archive/rrutter) will
not be updated anymore. This means R is frozen with version 2.15.3 and
the packages available will not be updated on CRAN or the RRutter PPA
for now.
At some point, likely around May 1st, I will move CRAN and the RRutter
PPA to version 3.0.0. This should give users plenty of time to remove
those repositories from apt so the upgrades do not occur. I will warn
everyone when I am about to do this.
The one exception to this rule will be the forth coming Ubuntu 13.04
(Raring Ringtail). When I add this release to CRAN and the PPA, I will
be using R 3.0.0 and packages built against 3.0.0.
**R 3.0.0 and recommended packages will be available on RDev PPA**
If you do want to upgrade R to 3.0.0, you can use my [RDdev
PPA](https://launchpad.net/~marutter/+archive/rdev). This will have the
latest version of R and the recommended packages built against it.
Instructions on how to install the PPA are available at the [RDdev
PPA](https://launchpad.net/~marutter/+archive/rdev) webpage. As of
right now, only 12.10 (quantal) builds are available, but others will be
added when bugs are worked out. Please, do not have the RDev PPA and
(CRAN or RRutter PPA) enabled at the same time, as that could cause issues.
**What about c2d4u?**
Excellent question.
**Stopping support for Hardy and Oneiric**
Both Hardy (8.04) and Oneiric (11.10) are ending support in April 2013.
Therefore, I will not be updating any version of R for these releases.
I, for one, am happy to finally be able to rid myself of the albatross
(or should I say heron) that is Hardy. I will not delete these files
for a while, but there will be no further updates. Support for Lucid
(10.04) will continue until April 2015 or until something becomes very
broken.
**Are you sure you don't have anything to say about c2d4u?**
[c2d4u](https://launchpad.net/~marutter/+archive/c2d4u) is an ambitious
project that houses over 1000 packages for R as Ubuntu binaries that can
be installed via apt or synaptic. You should really check it out. It
has great packages like RCpp and ggplot2, among others.
My first priority will be is to build all the packages for Ubuntu 13.04
(Raring Ringtail) using R 3.0.0. After that is complete, I will start
rebuilding the packages for 12.04 (Precise), the latest LTS, against
3.0.0. If I still have any patience left, I will convert the 12.10
(Quantal) packages over.
If you have any questions, please email me.
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
_______________________________________________
R-SIG-Debian mailing list
R-SIG-Debian at r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-debian
--
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre
Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB
http://nebc.nerc.ac.uk
+44 1491 69 2705
More information about the Bio-linux-list
mailing list