Compilation of R packages

| Le Mercredi 5 Juillet 2006 09:41, Dirk Eddelbuettel a ?crit?:
| > Salut Vincent,
| >

| > | I'm currently following your procedure suggested on R-SIG-Debian
| > | (https://stat.ethz.ch/pipermail/r-sig-debian/2006-June/000095.html) to
| > | compile and install the latest version of R on Kubuntu. It is my
| > | understanding that I can't just use Debian unstable's binary packages
| > | (which is too bad).
| >
| > It may be worth trying. Debian unstable may well be ahead in terms of
| > certain libraries but you can try.
| 
| Just tried installing r-base from Debian unstable. It requires updating libc6 
| (from 2.3.6-0ubuntu20 to 2.3.6-15). I cancelled the operation in fear of 
| wrecking my newly installed system havoc.

Probably prudent. I still don't have a good feel for where/how Ubuntu and
Debian are apart in their binary underlyings (and also somewhat frustrated
Ubuntu deviated, but that's for another time, and I even run Ubuntu on some
boxen).
 
| > I run Kubuntu at home on the `terminal/workstation' machine that has my
| > screen and keyboard, but I tend not to run R on that one but rather on a
| > Debian testing server I also keep around.  At work, I run Ubuntu and just
| > downloaded the sources from Debian unstable onto Ubuntu 5.10 and rebuilt
| > (which required one change in debian/control to remove the Depends and
| > Build-Depends on gfortran from a versioned Depends to an unversioned
| > Depends).
| 
| This is exactly what I did (except the modifications to debian/control) and 
| triggered my question. Building r-base builds r-recommended, but not the 
| r-cran-* packages r-recommended depends on.

Yes.

A few years ago I decided to decouple r-base and r-recommended. I now update
r-cran-* whenever new files ones appear on CRAN, and that includes the
package that the 'virtual' r-recommended Depends on.  So in short: you don't
get the underlying r-recommended packages when you build r-base from
_unstable_ or _testing_.

You do get them if you rebuild from the Debian stable backport at CRAN that
Christian takes care of.  

| Then it seems that building of 
| the r-cran-* packages must be done in a specific order.

Yes. At the R package level there is a tricky net of interdependence. You
need to figure that out.

Or, as I suggested to your first email, forget all the futzing and just use
R itself as in 

	install.packages(c("nlme", "VR", "boot", "lattice", ...),
                         depend=TRUE)

and R will sort it out.  As r-base-core only 'Recommends: r-recommended" you
should be fine.


| > | All went well for the r-base* packages. Compiling the packages
| > | r-recommended depends on seems to be another piece of cake. First, I had
| > | to download the source packages one by one (boot, cluster, ..., vr).
| > | Second, it looks like the packages have to be compiled and installed in a
| > | very specific order to solve dependency problems.
| > |
| > | Would you be kind enough to outline the specific procedure you follow to
| > | compile all the R packages for debian? Perhaps do you even have a script
| > | I might use.
| >
| > The r-sig-debian message you reference is 'defensive' in the sense that it
| > works on Debian stable and other other releases with compilers, libraries,
| > ... that may be a few months and releases old.  You didn't say which
| > Kubuntu you are running 
| 
| The latest, Dapper Drake (6.06).
| 
| > -- but you may not have to follow Christian's way 
| > as implemeneted in the stable port (and hence his way of dealing with
| > r-recommended as a big 'sumo' package). You could just install the CRAN
| > packages directly, or build from my Debian unstable sources (instead of
| > rebuilding on CRAN) -- a more 'offensive' approach.
| >
| > Anyway, as to why that particular way failed and what you may do about it
| > ... let me CC this to Christian who is probably in a better position to
| > answer this.
| >
| > And as a general rule, may be better to ask this on r-sig-debian as other
| > may have $0.02 (Canadian :) to chip in as well.
| 
| This reply is CCed to the list.
| 
| > Lastly, we should probably update the README on the CRAN site with some
| > recommendations for Ubuntu users. Something to discuss on r-sig-debian?
| 
| As (K)Ubuntu seem to become increasingly popular flavours of Debian, it would 
| certainly be worth adding a note. Or perhaps someone might be interested to 
| maintain up-to-date Ubuntu packages of R?

Volunteers are always welcome.  This may be as easy as taking Christian's
fairly self-contained 'Debian stable' packages from CRAN and re-building
those on (K)Ubuntu 06.06 for CRAN...
 
| ...
| 
| Look, 
| 
| 1) I have no experience whatsoever in maintaining Debian/Ubuntu packages;
| 2) I do not know exactly how more recent versions of packages are distributed 
| for Ubuntu;
| 
| however, if nobody else with more experience than I is interested to maintain 
| such packages, I might try to do my part. I'll just need a mentor. ;-)

I think Christian and I would be happy to mentor you.  It;s all pretty
scriptable and based on things that are documented somewhere. The key is
knowing where :)

Dirk

 
| Bye!   Vincent
| 
| > Dirk
| >
| > | Thanks a lot in advance!
| > |
| > | Cordialement,
| > |
| > | --
| > |   Vincent Goulet, Professeur agr?g?
| > |   ?cole d'actuariat
| > |   Universit? Laval, Qu?bec
| > |   Vincent.Goulet at act.ulaval.ca   http://vgoulet.act.ulaval.ca
| 
| -- 
|   Vincent Goulet, Associate Professor
|   ?cole d'actuariat
|   Universit? Laval, Qu?bec 
|   Vincent.Goulet at act.ulaval.ca   http://vgoulet.act.ulaval.ca

Hell, there are no rules here - we're trying to accomplish something. 
                                                  -- Thomas A. Edison