Le Mercredi 5 Juillet 2006 09:41, Dirk Eddelbuettel a ?crit?:> Salut Vincent, > > On 4 July 2006 at 23:27, Vincent Goulet wrote: > | 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.> 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. Then it seems that building of the r-cran-* packages must be done in a specific order.> | 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 runningThe 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? ... 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. ;-) 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
On Wed, Jul 05, 2006 at 11:53:42AM -0400, Vincent Goulet wrote:> Le Mercredi 5 Juillet 2006 09:41, Dirk Eddelbuettel a ?crit?: > > Salut Vincent, > > > > On 4 July 2006 at 23:27, Vincent Goulet wrote: > > | 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.Did you try to install the sarge backport packages? Those do not require updated libc6 packages, so perhaps they work on ubuntu?> 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. Then it seems that building of > the r-cran-* packages must be done in a specific order.[...]> 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?I did not see the question/problem?> 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 don't have an Ubuntu box, as I do not use Ubuntu at all. I guess I might find the space to setup an ubuntu chroot, but that would require some more convincing and time (so definetely not before sunday)! I think the sarge backported packages should be installable on ubuntu systems, and if not, you could simply use the sources I prepared for the backports and try building with them on Ubuntu. That's exactly what I would do if I had an Ubunto chroot. Get the source from your favourite CRAN mirror or directly from my debian page, this should work in /etc/apt/sources.list deb-src http://people.debian.org/~cts/debian stable/ apt-get source r-base, install the build-depends, and build the package (dpkg-buildpackage -rfakeroot or debuild). As Dirk said, I changed the r-recommended package to include all r-cran-* packages to make the maintenance of the backport easier for me. Actually, Dirk suggested this when I started the backport. This is a little tricky for upgrading since r-cran-* packages are only overwritten but not removed, but I think we solved most problems there (just an installation problem, no problems with running the packages). If you run into those problems, the cleanest way is to remove the currently installed r-recommended (and with it r-base), and then install the packages from the backport. BChristian
On 5 July 2006 at 11:53, Vincent Goulet wrote:
| Le Mercredi 5 Juillet 2006 09:41, Dirk Eddelbuettel a ?crit?:
| > Salut Vincent,
| >
| > On 4 July 2006 at 23:27, Vincent Goulet wrote:
| > | 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