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 [email protected] (630)840-6468
Fermilab ComputingDivision/LCSI/CSI LMSS Group
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