On Thu, 15 Nov 2007, Paul Johnson wrote:

> I have a script that I run every night and it checks for a long list
> of R packages and installs what is needed.  On a new SL5 system, I
> noticed that the script failed because the package "coda" was not
> available.  "There's a mistake" I thought to myself, because coda is
> one of the heavily used packages for Bayesian MCMC modeling.
>
> It turned out that the CRAN current version of coda is set to ONLY
> compile for R >= 2.5.  Since the SL5 version of R is 2.4, the package
> manager was not able to find the coda package.  I updated R on the
> system to the version that is available in Fedora and then the package
> script worked fine.
>
> I understand the SL5 philosophy of preferring stable things, but since
> R is one of the "feature packages" that differentiates Scientific
> Linux from other RedHat EL descendants like CentOS, it seems important
> to me that you should keep R more up to date than most packages.
>
> I went to the SL website to try to enter this opinion, but I find it
> is necessary to log in and I can't find a place where I can register
> myself.  What's up with that?

SL currently provides R-2.5 in the 'testing' repository, so something 
like:

   yum --enablerepo=sl-testing update R

should pick up the newer version (and not pull in any other unrelated 
testing updates).

I say *should* 'cos we upgraded to the 'testing' R some time ago so I 
can't trivially test that I got the yum options right.  Apologies if I 
did.

Troy sent a message to the list the other day saying that he plans to 
include an updated R in each new release of SL so SL51 will probably have 
something fairly recent by the time it is released.

Troy Dawson <[log in to unmask]> wrote:

> I have thought of a plan for R.
> The problem is that we have two sets of users.  Those that want the 
> latest R and those that want the stable, this is what we use R.
>
> As each S.L. release comes out, we'll just check and see what the latest 
> R is, and put it in that release.
> But we don't update the R in the older releases. So if a person wants to 
> sit on whatever R came with S.L. 4.5, they can just stay at S.L. 4.5. 
> Or just use the R in S.L. 4.5 and put it in their excludes line for
> yum.
> 
> This will allow us to get a new version out every 6 months, which should 
> keep at least a fair amount of the R users happy, I hope.

I think that 6-monthly updates will certainly keep R fresh enough for our 
users - they seem to start complaining if it is more than 12 months old... 
:-)

-- 
Jon Peatfield,  Computer Officer,  DAMTP,  University of Cambridge
Mail:  [log in to unmask]     Web:  http://www.damtp.cam.ac.uk/