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.
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 ?
2) I can't compile from source code without secret sauce?
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.
Cheers
Paul
-----Original Message-----
From: Dirk Eddelbuettel <e...@debian.org>
To: Michael Rutter <ma...@psu.edu>
Cc: Paul Leo <p....@uq.edu.au>, Douglas Bates <ba...@stat.wisc.edu>,
r-sig-debian <r-sig-debian@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
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