Eva Myers wrote:
> Dear All,
> Over the past month or two, I've been having problems updating R from
> the UK mirror of the CRAN repository.  I have the R repository
> enabled:
> 
> 
> sirtommy 13:41% more /etc/yum.repos.d/R.repo
> [R]
> name=CRAN R repository
> baseurl=http://www.stats.bris.ac.uk/R/bin/linux/redhat/el5/i386/
> enabled=1
> gpgcheck=0
> gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-csieh file:///etc/pki/rpm-gpg/RPM-GPG-KEY-dawson file:///etc/pki/rpm-gpg/RPM-GPG-KEY-jpolok file:///etc/pki/rpm-gpg/RPM-GPG-KEY-cern
> 
> 
> However, "yum update" has persistently refused to update R, which has
> remained stuck at version 2.9.0 rather than the latest version 2.9.2.
> "yum clean all" makes no difference.
> 
> On one of my SL52 machines I have done some further experiments, but
> they didn't solve the problem.  I tried "yum install R-core" but got
> the error message
> 
>  --> Missing Dependency: perl(File::Copy::Recursive) is needed by
>      package R-core-2.9.2-1.el5.i386 (R)
> 
> That was resolved by installing the required perl package from the dag
> repo, but the next attempt to install R-core gave a stream of error
> messages about file conflicts, for example
> 
>   file /usr/lib/R/library/utils/html/example.html from install of
>   R-core-2.9.2-1.el5 conflicts with file from package R-2.9.0-1.rh5
> 
> After I uninstalled the R-2.9.0 package, R-core would install, but
> "yum install R" found only the old R from sl-base, as did "yum list
> R":
> 
> 
> sirtommy 13:46% yum list R
> Loaded plugins: kernel-module, protect-packages
> Available Packages
> R.i386                           2:2.7.0-1.sl5                           sl-base
> 
> 
> What should I do to install R 2.9.2 from CRAN?
> Eva.

Hi Eva,
I bet it stems from us having a epoch of 2 in our version of R.
That stems back from the first time we compiled R, I didn't see that we 
had an epoch of 2.  I didn't notice that we had the epoch until I was 
reading the spec file from Fedora or EPEL, which has the epoch in, with 
a note saying they had to do it because Scientific Linux had it. Once 
you have an epoch, it's almost impossible to get it out.

But how to fix your problem?
You need to exclude R that is coming from Scientific Linux.  That's not 
too hard.  You need to add the following at the end of 
/etc/yum.repos.d/sl.repo and /etc/yum.repos.d/sl-security.repo

exclude=R R-devel libRmath libRmath-devel

That should keep it from trying to install Scientific Linux's R.

Troy

-- 
__________________________________________________
Troy Dawson  [log in to unmask]  (630)840-6468
Fermilab  ComputingDivision/LCSI/CSI LMSS Group
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