[R-sig-Debian] Upgrading to R 2.5.1 on Ubuntu Feisty 64
Vincent Goulet
vincent.goulet at act.ulaval.ca
Thu Jul 26 19:54:23 CEST 2007
Bonjour Christophe et al.,
As has been previously said, I compile R packages for i386 only (I
don't have access to another architecture). There has been
discussions recently that someone might take responsibility of 64 bit
pacakges preparation, but I don't know more.
The i386 packages are very up-to-date with the Debian ones.
Now, if you want to compile your own packages from the sources, you
may find useful to have a look (or use) my build (bash) scripts. They
will show you which modifications I make before compiling and all the
commands you need to issue. The scripts are located here:
https://vgoulet.act.ulaval.ca/svn/R/cran-bin/
The *-cran.sh scripts are used to build the r-cran-* packages and the
*-base.sh scripts to build the base R packages.
My setup is the following: I have Dapper, Edgy and Feisty installed
in chroot jails where the packages are built. I invoke one update-r-
*.sh script and it goes through each jail in turn executing the build-
r-*.sh script.
Hope this helps!
Vincent
Le 07-07-26 à 11:46, Johannes Ranke a écrit :
> 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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>>
>> --
>> Three out of two people have difficulties with fractions.
>>
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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
>
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---
Vincent Goulet, Professeur agrégé
École d'actuariat
Université Laval, Québec
Vincent.Goulet at act.ulaval.ca http://vgoulet.act.ulaval.ca
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