[R-sig-Debian] Upgrading to R 2.5.1 on Ubuntu Feisty 64

[Johannes Ranke]

Hi Dirk and Christophe,

Vincent has feisty packages for R 2.5.1, but not for amd64. Probably all
architecture independent packages got installed, but not the binaries.

I have a section in the Debian README on CRAN that says:

	We only have binaries for the i386 and amd64 architectures. You can
	use the source packages from

	   deb-src http://<favorite-cran-mirror>/bin/linux/debian stable/

	to compile binaries for other platforms.

So in this case, if you need to rebuild R 2.5.1 from CRAN on amd64, use

	   deb-src http://<favorite-cran-mirror>/bin/linux/ubuntu feisty/

then do an 

    sudo apt-get build-dep r-base

and

    sudo apt-get source -b r-base

then

    cd ..

and install the debs you find there. In case you want to build some of
the recommended packages, be sure you installed the new r-base-dev.

The script I use to build all recommended packages (only architecture
dependent debs) is here:

	http://kriemhild.uft.uni-bremen.de/viewcvs/build_recommended_etch.sh?root=r-backports&view=markup

Some parts of this script you will probably want to adapt, if you use
it.

Cheers,

Johannes

* Dirk Eddelbuettel <edd at debian.org> [070726 16:50]:
> 
> Hi Christophe,
> 
> Thanks for posting here -- this should give you the audience for R
> questions on Debian / Ubuntu.  I do use Ubuntu at work, but as
> maintainer of the package I do know its structture and simple rebuild
> (on x86).
> 
> I think Johannes and Vincent have published sets of (Python?) scripts
> that automate fetching the package source and locally rebuilding.  For
> small packages with small built-dependencies, this can be as trivial
> as a single apt-get call.  For R it is typically not much more work,
> but R 2.5.1 did switch to compiler gcc-4.2 etc, so this time you need
> to do minimal editing of debian/control (to reduce the Build-Depends)
> and debian/rules (to undo the compiler setting from gcc-4.2 to gcc,
> same for g++, gfortran).
> 
> That should be all. I hope others can pitch in with tips. I am a
> little pressed for time right now or I'd try to cook up a tutorial --
> we should create one on the R or Debian or Ubuntu wikis as this
> package rebuilding is generally useful.  Also do look if there are
> generic 'backporting' tutorials somewhere for Debian that show the
> mechanics.
> 
> Please give it a try and post questions here.
> 
> Cheers, Dirk
> 
> 
> On Thu, Jul 26, 2007 at 11:57:12AM +0200, Christophe Bonenfant wrote:
> > Hi there,
> > 
> > A new thread was started on the R list about problems to upgrade R to
> > version 2.5.1 and we were re-directed on this list. We are two with
> > exactly the same problem and the same distribution (Ubuntu Feisty 64).
> > We are unable to upgrade to R 2.5.1. The r-base-core package is version
> > 2.4.1 in Ubuntu repositories while all others r-cran related packages
> > are upgraded to R 2.5.1 (r-base-dev,r-base...). This doesn't seem to be
> > the case for the 32-bits version.
> > 
> > Do you have any tips to go through this? Thanks.
> > 
> > Christophe
> > 
> > Details:
> > 
> > $ uname -a
> > 
> > Linux bronski 2.6.20-16-generic #2 SMP Thu Jun 7 19:00:28 UTC 2007
> > x86_64 GNU/Linux
> > 
> >   > R.version
> >                  _
> > platform       x86_64-pc-linux-gnu
> > arch           x86_64
> > os             linux-gnu
> > system         x86_64, linux-gnu
> > status
> > major          2
> > minor          4.1
> > year           2006
> > month          12
> > day            18
> > svn rev        40228
> > language       R
> > version.string R version 2.4.1 (2006-12-18)
> > 
> > $ cat /etc/apt/sources.list
> > 
> > ...
> > 
> > ## Clé : gpg --keyserver subkeys.pgp.net --recv-key E2A11821
> > ## puis : gpg -a --export E2A11821 | sudo apt-key add -
> > deb http://cran.univ-lyon1.fr/bin/linux/ubuntu feisty/
> > #deb http://cran.cict.fr//bin/linux/ubuntu feisty/
> > 
> > ...
> > 
> > 
> > -- 
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-- 
Dr. Johannes Ranke                 jranke at uni-bremen.de     Key ID: F649AF90
UFT Bremen, Leobenerstr. 1         +49 421 218 63373
D-28359 Bremen                     http://www.uft.uni-bremen.de/chemie/ranke