[R] R and Debian Linux

Dirk Eddelbuettel edd at debian.org
Fri Nov 2 03:14:34 CET 2007


On 2 November 2007 at 00:21, (Ted Harding) wrote:
| Hi Folks,
| Lately I've been testing out recent versions of various
| Linux distributions, preparatory to choosing which one
| I want to upgrade to.
| One of these is debian 4.0 ("Etch").
| I can install R on it as a debian package (it comes
| through as "R version 2.4.0 Patched (2006-11-25 r39997)".

Also note that CRAN has so-called 'backports' of the current R version
(i.e. now 2.6.0) to both Debian stable (aka "etch" right now) and different
Ubuntu versions -- see $CRAN/bin/linux/{debian,ubuntu}.

| Many of the extra packages are also present as debs,
| and install and perform without problems.
| But I've also tried installing some other packages,
| not available as debs, from sources on CRAN.
| Here I encounter a show-stopper: "gfortran not found".

For package building on Debian and Ubuntu, _always_ install r-base-dev as it
covers this via the Depends mechanism.

| It turns out that the only reference to "gfortran"
| available in the list of packages available in the
| debian repositories is "libgfortran". The full

Err, no, there's way more. For me on testing aka "lenny":

   edd at ron:~> apt-cache search gfortran | wc -l
   edd at ron:~>  

Anyway, you want gfortran-4.1 (or maybe gfortran-4.2, see what;s encoded in
/etc/R/Makeconf, and in any event, r-base-dev will do the Right Thing.

| package "gfortran" is not available, so there is
| no fortran compiler callable as gfortran.
| On the other hand, I find it is available for Ubuntu
| (7.04) -- the full gfortran -- and I can successfully
| compile and install these other packages. Yet Ubuntu
| is also Debian based (apparently a more recent version,
| though I can't make out which).

Easy. Debian 4.0 was release before Ubuntu 7.06 (aka June 2007) and Ubuntu
7.10 (aka Oct. 2007) so there can be differences.  Also don't ignore that
Canonical / Ubuntu do have a slightly different motivation / agenda.

| I've been to the CRAN section which deals with precompiled
| Debian binaries:
|  http://www.stats.bris.ac.uk/R/bin/linux/debian/
| When I follow the advice:
|   "Simply add something like
|  deb http://<favorite-cran-mirror>/bin/linux/debian stable/

Works for me. You did replace <favorite-cran-mirror> with something like
cran.uk.r-project.org, right?
|   to the file /etc/apt/sources.list on your computer and
|   install as usual."
| I get an error message that this is "malformed". So I find
| myself somewhat stuck when trying to use R to the full on
| the Debian distribution. Since I'm not particularly familiar
| with the ways of Debian yet, I'm not getting any diagnostic
| ideas either. But I do get an impression that there's a bit
| of a mis-match somewhere between R and Debian!
| Does anyone have any good hints about all this?

Yes, the r-sig-debian list is the place for this. You need subscribe before
you can post.
| [BTW, I'm trying these out as guests in virtual machines,
| using virtualbox, which seems to me to run very well]

[ I heard there were some NAT/networking issues to go 'both ways' towards the
hosted systems? ]

Hope this helps, and that you find Debian a useful platform for R work.  If
you have suggestions for improved or clarified documentation, please do not
hold back, preferably via patches.

Thanks, Dirk

Three out of two people have difficulties with fractions.

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