[R] Problem with RHEL 5 repo and the latest R RPMs

Martyn Plummer plummer at iarc.fr
Tue Aug 25 10:51:48 CEST 2009


It turns out that the default checksum for "createrepo", the command
that creates repository metadata, has changed from sha1 to sha256,
whereas Enterprise Linux 5 still requires sha1. I have modified the
scripts to use the older checksum for EL4 and EL5.

Sorry for the slow reply. Lance Brown from Duke University already
raised this problem with Bob Kinney and me.  When I saw a query from
Hugh Brown I was not paying enough attention to see that you were
somebody else.  

Martyn 

On Fri, 2009-08-21 at 14:23 -0500, Marc Schwartz wrote:
> 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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