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

Mon Apr 6 14:22:37 CEST 2009

On Sun, Apr 5, 2009 at 10:32 PM, Vincent Goulet
<vincent.goulet at act.ulaval.ca> wrote:
> Le dim. 05 avr. à 21:53, Paul Leo a écrit :
>
>> Thankyou Dirk,
>> That was a great summary I think I understand the philosophy now. I will
>> go move forward with compiling the source code with caution.
>
> (Phew, shouldn't have been away today! Sorry folks, but I'll sort of reply
> to many messages at once.)
>
> First, Paul, if you want to compile R on Ubuntu from the Debian sources,
> you'll want to use or, at least, have a look at my build scripts located at:
>
>        https://vgoulet.act.ulaval.ca/svn/R/cran-ubuntu/
>
> (This is the public svn repository Dirk was referring to.) The important one
> is build-r-base.sh; the script makes all the modifications to the Debian
> sources needed to compile on Ubuntu releases from Dapper to Intrepid and
> then launches the build process.

> Regarding the distribution of binary packages of beta versions of R for
> Ubuntu, I fully agree with Michael.

> I also think Doug's proposal to distribute patched sources is a nice
> compromise. That said, I'm not too sure which files I should make available.
> Dirk may confirm that the needed files would be, for example:

>        r-base_2.9.0~20090327-1intrepid0.diff.gz
>        r-base_2.9.0~20090327-1intrepid0.dsc
>        r-base_2.9.0~20090327-1intrepid0_i386.changes
>        r-base_2.9.0~20090327.orig.tar.gz

If I recall correctly you only need to make the .dsc, .orig.tar.gz and
.diff.gz files available.
> I never noticed at which stage of the build process the first three files
> are created. Is it possible to create them without fully compiling the
> package?
>
> Cheers,
>
> Vincent
>
>> 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
>> |
>>
>>
>>        [[alternative HTML version deleted]]
>>
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