[Bio-Linux] [Fwd: [R-sig-Debian] Moving to R 3.0.0 on Ubuntu]

Fri May 3 05:11:49 EDT 2013

Dear R users,

Further to my last message, Michael Rutter is now in the process of
upgrading the R packages to 3.0.0.  As far as I can tell, the upgrade
will be fairly smooth with the following important caveats:

1) All locally installed modules will need to be refreshed and rebuilt
by the system administrator (or the user if installed in the home dir).
Users of Bioconductor in particular will need to do this.  See the notes
here:

http://nebc.nerc.ac.uk/tools/bioinformatics-docs/other-bioinf/r-and-bioconductor#rpack

2) I have prepared updated DEB packages for all the R libraries that
install this way, but there may be a day or two when these are out of
sync with the core R packages.  You will then see warnings from the
update manager that updates cannot be applied.  Give it a couple of days
and this should all be straightened out.

If you are not sure if this applies to you then there's no need to be
paranoid.  R will complain loudly and clearly if you try to load an
incompatible module, and you will be in no doubt that you need to update
it.

Cheers,

TIM

On Thu, 2013-03-28 at 09:42 +0000, Tim Booth wrote:
> 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
> 
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> 

-- 
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