On Aug 21, 2009, at 1:00 PM, Hugh Brown wrote:
Hi everyone -- I have a number of systems here running CentOS 5.2 and
5.3. Recently, I tried adding a package unrelated to R and found that
yum is complaining about the R repo. Here's the error I get when
running yum update:
----
$ sudo yum update
[snip]
http://cran.r-project.org/bin/linux/redhat/el5/x86_64/repodata/primary.xml.gz
: [Errno -3] Error performing checksum
Trying other mirror.
primary.xml.gz 2.9 kB 00:00
http://cran.r-project.org/bin/linux/redhat/el5/x86_64/repodata/primary.xml.gz
: [Errno -3] Error performing checksum
Trying other mirror.
Error: failure: repodata/primary.xml.gz from CRAN: [Errno 256] No
more mirrors to try.
----
/etc/yum.conf has these lines:
----
# PUT YOUR REPOS HERE OR IN separate files named file.repo
# in /etc/yum.repos.d
[CRAN]
name=CRAN
baseurl=http://cran.r-project.org/bin/linux/redhat/el5/x86_64
----
This error persists even after running "yum clean all" and "rm -f
/var/lib/rpm/__db.00? ; rpm --rebuilddb". I've disabled the CRAN repo
and applied all available updates, and I still get these problems.
I've checked with the folks at CentOS, and they suggested contacting
the repo manager.
Looking at the repo itself, it seems that there's a new version that
was uploaded 10 days ago; I'm wondering if the new package or repo
files are causing me problems somehow.
Has anyone else had this problem? Is there something I need to do to
make updates work?
Please let me know if you need any further information, or if there's
another person or mailing list I should be contacting.
Thanks in advance for any help!
Hugh,
Take a look in /etc/yum.repos.d and see if there are any other yum
config files (*.repo) with enabled repos that may be conflicting with
the config you have in /etc/yum.conf.
You can use:
sudo yum repolist
to get a quick list of repos that are enabled by default.
I would also remove the CRAN config from /etc/yum.conf and unless
there is already one in /etc/yum.repos.d, create another (eg.
CRAN.repo file) just for CRAN with the appropriate config information,
including an explicit 'enabled=1' or 'enabled=0' directive. For
several Fedora/RHEL releases, having separate yum config files, one
per repo, is the preferred model.
An alternative, would be to not use the CRAN repo and add the EPEL (https://fedoraproject.org/wiki/EPEL
), which has R and other add-on packages that are not part of the
default RHEL/CentOS distribution. Instructions on how to set up and
use the EPEL are on the page linked above.
I am also cc:ing Martyn Plummer and Bob Kinney here, just in case they
have other ideas or are aware of other issues that may be relevant.
HTH,
Marc Schwartz
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