Jon Peatfield wrote:
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 <[EMAIL PROTECTED]> 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... :-)
Here is what I sent to scientific-linux-devel
-------------------
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.
--------------------
Just so you know, I have put R 2.5.0 into rolling, it should go out with the
beta, and I am working on R 2.6.0. It didn't compile on the first shot, so I
need to check and see why. Hopefully it's something trivial. If I get it to
compile before the beta goes out, I'll put it in.
Troy
--
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Troy Dawson [EMAIL PROTECTED] (630)840-6468
Fermilab ComputingDivision/LCSI/CSI DSS Group
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