[R-sig-Debian] Are there Debian/Ubuntu packages of the betaversions of R-2.9.0

Mon Apr 6 05:15:12 CEST 2009

Hi Paul,

On 6 April 2009 at 11:53, Paul Leo wrote:
| Thankyou Dirk,
| That was a great summary I think I understand the philosophy now. 

Pleasure! It was a very valid question qestion.

| I will go move forward with compiling the source code with caution. 

This list may actually be the best place to start assembling 'best practices'
for coping with several installed versions, in one wants to, on Debian /
Ubuntu.  I guess some people just install into /usr/local/lib/R-$version and
then set the path on the fly, but I am not sure how to best deal with a
common (or separate ?)  R_LIB paths -- I personally don't need multiple
versions at the same time :-) so I don't spend much time there.

But it may make sense to, say, start taking some HOWTO notes on
wiki.r-project.org or some other place. 

As it might for, say. ways to combine Debian CRAN packages with CRAN packages
etc.  All of this is somewhat underdocumented....

Cheers, Dirk

| Cheers
| Paul
| 
| -----Original Message-----
| From: Dirk Eddelbuettel <edd at debian.org>
| To: Paul Leo <p.leo at uq.edu.au>
| Cc: Dirk Eddelbuettel <edd at debian.org>, Michael Rutter <mar36 at psu.edu>,
| Douglas Bates <bates at stat.wisc.edu>, r-sig-debian
| <r-sig-debian at r-project.org>
| Subject: Re: [R-sig-Debian] Are there Debian/Ubuntu packages of the
| betaversions of R-2.9.0
| Date: Sun, 05 Apr 2009 19:29:26 -0500
| 
| 
| On 6 April 2009 at 10:04, Paul Leo wrote:
| | I not sure what the problem is but I'm a new ubuntu user , so forgive my
| | ignorance.. Why can I not have a stable and development version of R
| | installed and go between them as I wish? The library path includes the R
| | version number; can the binaries not go to /usr/local/R2.9 ? Guess I am
| | not sure what the problem is. 
| 
| /usr/local/ is yours, /usr is for the packaging system.  That is a strict
| boundary that is never crossed.
| 
| Under /usr, the current package lives in one place and does therefore not
| allow multiple versions.  In theory, what you suggest is perfectly
| feasible. Emacs does it, and many other apps allow to have multiple versions
| installed. I once engineered the same rewrite to have several Octave versions
| installed.  It is possible --- but it also requires a more-or-less complete
| rewrite of the package infrastructire, and then tests, of all associated
| scripts and files. I will have to leave that for other volunteers as I don;t
| have the time to drive that change.
| 
| So in the short run, go with your own builds in /usr/local if you need
| several versions at the same time.
| 
| | Yes all the Bioconductor development version is on R 2.9. There are many
| | thousands of bioconductor users who stay on the development version of
| | R . This is where I prefer to be, this was easy with windows,  I could
| | install as many versions of R as I like 2.7, 2.8.1, 2.9 .... The
| | bioconductor libraries are smart enough to know the R version you are
| | running  and use the correct repositories for their libraries. But that
| | is the dark ages I don't want to return to!
| | 
| | The option of a virtual install seems unnecessary surely ? I am familiar
| | with that but I don't want to chop up my memory of each instance as I
| | need it all for some jobs.
| | 
| | As you can tell this is my first foray into this topic and I certainly
| | don't to put any more demands on you time. I guess I did not realise it
| | was either one or the other 2.8.1 or 2.9.0 ? I did not anticipate that.
| | Is the reason just trivial , same excutable names and default install
| | path or is there more to it?
| | 
| | I do not mind compiling from source etc; actually part of joining this
| | email group was to get a sense of what was the "standard approach" that
| | is used for ubuntu and development versions of R. I also wanted to get a
| | feel for ess compatibility with the development version of R. 
| | 
| | So summary
| | 1) I can't just install the stable and development versions  from deb
| | files and have them play nice ?
| 
| Sure. But not from .deb files as you can have exactly one R binary at the
| same time.
| 
| [ But you can use that for the default R and then keep a bleeding edge one in
| /usr/local too. ]
| 
| | 2) I can't compile from source code without secret sauce?
| 
| Sure you can. It just won't be as integrated as the pre-packaged version.
| 
| | I don't agree there should be a test for who can use the ubuntu
| | development version , it is development and unstable as so no one can
| | reasonable expect it to be foolproof. General direction are all that
| | anyone could reasonably expect.
| 
| Most of us do not perceive Ubuntu to be the 'developer distro'.  It really is
| easy enough to split this over several different machines too.  I.e. under my
| desk is an Ubuntu box driving the desktop and a headless Debian box
| supporting additional development work.  There are many possible approaches.
| What we attempt to provide for Ubuntu is a mainstream package to satisfy
| users of the _currently released_ R versions.
| 
| Everybody is invited (and welcone) to start their own project for packages of
| a development version.  But I think you just cannpt expect already-busy
| volunteers like Vincent, Michael or myself to do it for you.
| 
| Cheers, Dirk
|  
| | Cheers
| | Paul
| | 
| | -----Original Message-----
| | From: Dirk Eddelbuettel <edd at debian.org>
| | To: Michael Rutter <mar36 at psu.edu>
| | Cc: Paul Leo <p.leo at uq.edu.au>, Douglas Bates <bates at stat.wisc.edu>,
| | r-sig-debian <r-sig-debian at r-project.org>
| | Subject: Re: [R-sig-Debian] Are there Debian/Ubuntu packages of the
| | betaversions of R-2.9.0
| | Date: Sun, 05 Apr 2009 08:18:09 -0500
| | 
| | 
| | On 5 April 2009 at 08:36, Michael Rutter wrote:
| | | If we make the beta debs of R available for Ubuntu, I think they
| | | should be in a separate repository, as not to be pushed to people
| | | uncomfortable with beta software.  If we went down this path, we could
| | | also limit ourselves to the latest Ubuntu release as well as the
| | | latest long term service release versions of Ubuntu.
| | | 
| | | I do not use bioconductor, so I have to ask how many packages are
| | | built in the approximately one month period the R beta is available
| | | for public release?   I visited the web site, and there is a devel
| | | branch.  Are all of those packages built against R 2.9?
| | | 
| | | My personal opinion is that we should not follow the google definition
| | | of beta, and reserve the tag for testing purposes.  If you want to
| | | test the beta version, there should be a minimum amount of "expertise"
| | | required for entry.  For Ubuntu, having to compile from source could
| | | be that bar.  We could supply directions on how to build from the deb
| | | source packages.  It would probably need a script that makes the
| | | corrections needed to compile under Ubuntu.
| | 
| | I agree. I think we should not push down 2.9.0 on all Ubuntu users. 
| | 
| | Paul, given that Debian does have the 2.9.0 deb files ready
| | for the picking, you could also try a chroot or virtual machine running
| | Debian unstable.  By using a virtual machine (like virtualbox, very easy to
| | set up in stock Ubuntu) you get a way to have the bleeding edge software
| | running on your system without affecting the general stability of your
| | system.
| | 
| | Otherwise, take the Debian .deb source and ask us for help with local package
| | builds based on those source (as e.g. right now where Debian's package has a
| | debian/rules which uses dh_prep which you need to turn back to dh_clean etc
| | pp).  I sometimes do that at work (eg to get current Debian MPI packages onto
| | Ubuntu etc).
| | 
| | Dirk
| | 
| 

-- 
Three out of two people have difficulties with fractions.