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Installing R on RedHat EL 5

12 messages · Marc Schwartz, R P Herrold, Christos Hatzis

Original
Christos Hatzis
# 
Hi,

I am totally new to Linux and trying to install R and related tools.  I
downloaded the rpm files for el4/x86_64 from the CRAN repository and
tried to run rpm but it did not go through complaining about
dependencies.

Do all the listed rpm files need to be installed?  What is the order in
which these need to be installed?

I appreciate any help with this or any suggestions for alternate ways
for installing pre-compiled versions of R and the packages in RHL.

Thanks.
-Christos Hatzis
Marc Schwartz
#
On Nov 13, 2009, at 1:59 PM, Christos Hatzis wrote:

            

      
      
      
    

        
The easiest way is to use the EPEL, which is a yum repository for RHEL  
and CentOS.

There is more information here:

   http://fedoraproject.org/wiki/EPEL

with the key steps here in the FAQ:

   http://fedoraproject.org/wiki/EPEL/FAQ#howtouse

If you are on 64 bit RHEL, you will need to replace the 'i386' in the  
first command's path with 'x86_64':

   su -c 'rpm -Uvh http://download.fedora.redhat.com/pub/epel/5/x86_64/epel-release-5-3.noarch.rpm'

Then replace 'foo' in the second command with 'R', which will install  
R and any other dependencies that you may require:

   su -c 'yum install R'

Note that the latest version available appears to be 2.9.2 and I  
suspect that this is due to the imminent release of Fedora 12, which  
is presumably consuming Tom Callaway and others at the moment.

HTH,

Marc Schwartz

  
  


  


      

    

    

      
      

        


  

        

      Christos Hatzis
    

    

      
      #
    

  


  

      
Thank you Marc.
I will try this out.

-Christos

-----Original Message-----
From: Marc Schwartz [mailto:marc_schwartz at me.com] 
Sent: Friday, November 13, 2009 3:12 PM
To: christos.hatzis at nuverabio.com
Cc: r-sig-fedora at r-project.org
Subject: Re: [R-sig-Fedora] Installing R on RedHat EL 5

        
On Nov 13, 2009, at 1:59 PM, Christos Hatzis wrote:

        

            

      
      
      
    

        
The easiest way is to use the EPEL, which is a yum repository for RHEL  
and CentOS.

There is more information here:

   http://fedoraproject.org/wiki/EPEL

with the key steps here in the FAQ:

   http://fedoraproject.org/wiki/EPEL/FAQ#howtouse

If you are on 64 bit RHEL, you will need to replace the 'i386' in the  
first command's path with 'x86_64':

   su -c 'rpm -Uvh
http://download.fedora.redhat.com/pub/epel/5/x86_64/epel-release-5-3.noarch.
rpm'

Then replace 'foo' in the second command with 'R', which will install  
R and any other dependencies that you may require:

   su -c 'yum install R'

Note that the latest version available appears to be 2.9.2 and I  
suspect that this is due to the imminent release of Fedora 12, which  
is presumably consuming Tom Callaway and others at the moment.

HTH,

Marc Schwartz

  
  


  


      

    

    

      
      

        


  

        

      Christos Hatzis
    

    

      
      #
    

  


  

      
The installation seems to have gone through ok, but this is what I am
getting at the end:

--> Finished Dependency Resolution
R-devel-2.9.2-1.el5.x86_64 from epel has depsolving problems
  --> Missing Dependency: libX11-devel is needed by package
R-devel-2.9.2-1.el5.x86_64 (epel)
R-devel-2.9.2-1.el5.x86_64 from epel has depsolving problems
  --> Missing Dependency: pcre-devel is needed by package
R-devel-2.9.2-1.el5.x86_64 (epel)
R-devel-2.9.2-1.el5.x86_64 from epel has depsolving problems
  --> Missing Dependency: tk-devel is needed by package
R-devel-2.9.2-1.el5.x86_64 (epel)
R-devel-2.9.2-1.el5.x86_64 from epel has depsolving problems
  --> Missing Dependency: tcl-devel is needed by package
R-devel-2.9.2-1.el5.x86_64 (epel)
Error: Missing Dependency: tcl-devel is needed by package
R-devel-2.9.2-1.el5.x86_64 (epel)
Error: Missing Dependency: tk-devel is needed by package
R-devel-2.9.2-1.el5.x86_64 (epel)
Error: Missing Dependency: pcre-devel is needed by package
R-devel-2.9.2-1.el5.x86_64 (epel)
Error: Missing Dependency: libX11-devel is needed by package
R-devel-2.9.2-1.el5.x86_64 (epel)

Do I need to install other tools before running
su -c 'yum install R'? 

Thanks again.
-Christos

        
On Fri, 2009-11-13 at 15:11 -0500, Marc Schwartz wrote:

            

      
      
      
    

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Marc Schwartz
    

    

      
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Hmmm....that would suggest that yum is not picking up the default RHEL  
repos for some reason, as it would seem logical that those files would  
be there as opposed to the EPEL. Typically, yum will get any  
dependencies from all enabled and accessible repos.

As RHEL's repos for their binary RPMs are only available to folks who  
have paid for support, I am not sure how to best assist in getting the  
yum repo config RPM so that you can install or re-install it to  
confirm that the RHEL repo is configured and active.

One thing that you can check is to use:

   yum repolist

which should show you the current list of configured repos on your  
system and whether or not they are enabled. I suppose that it is  
possible that either the main RHEL binary repo is not configured on  
your system, it is not enabled or perhaps your system is being  
prevented from accessing it. You may have to run that command as 'root'.

An alternative, which has some risk, is to use the CentOS yum repos,  
which are supposed to be binary compatible with RHEL. The risk is that  
if you are in fact paying for RHEL support to RH, I would be hesitant  
to mix and match, if there is any risk of complications in the support  
contract.

Not having the 'devel' versions of the various RPMs will at some point  
cause you problems when installing source packages from CRAN.

A lot of the important details here are going to be dependent upon how  
you installed RHEL and whether or not there is a paid support contract  
in place for your installation.  If you have a SysAdmin that installed  
RHEL for you, he or she would be of help in resolving this.

HTH,

Marc

        
On Nov 13, 2009, at 2:52 PM, Christos Hatzis wrote:

        

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      R P Herrold
    

    

      
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On Fri, 13 Nov 2009, Marc Schwartz wrote:

        

            

      
      
      
    

        
no -- the package is ageing in their approvals queue -- more 
feedback will get it released sooner

-- Russ herrold

  
  


  


      

    

    

      
      

        


  

        

      Marc Schwartz
    

    

      
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On Nov 13, 2009, at 3:47 PM, R P Herrold wrote:

        

            

      
      
      
    

        
That's new within the past week or so:

   http://koji.fedoraproject.org/koji/packageinfo?packageID=1230

When I last checked in response to another recent query only 2.9.2 was  
there...

Thanks for the update Russ.

Marc

P.S. I am going to be away for the remainder of the evening (U.S. CST)

  
  


  


      

    

    

      
      

        


  

        

      Christos Hatzis
    

    

      
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Marc,

It seems that the RHEL is there and is active.  I'd rather stay with RHEL
since I do have purchased support.
I have started the process of registering the system with RHN so I will try
to see if system updates will solve the problem.  Will report back.

Thanks again.
-Christos

-----Original Message-----
From: Marc Schwartz [mailto:marc_schwartz at me.com] 
Sent: Friday, November 13, 2009 4:41 PM
To: christos.hatzis at nuverabio.com
Cc: r-sig-fedora at r-project.org
Subject: Re: [R-sig-Fedora] Installing R on RedHat EL 5

Hmmm....that would suggest that yum is not picking up the default RHEL  
repos for some reason, as it would seem logical that those files would  
be there as opposed to the EPEL. Typically, yum will get any  
dependencies from all enabled and accessible repos.

As RHEL's repos for their binary RPMs are only available to folks who  
have paid for support, I am not sure how to best assist in getting the  
yum repo config RPM so that you can install or re-install it to  
confirm that the RHEL repo is configured and active.

One thing that you can check is to use:

   yum repolist

which should show you the current list of configured repos on your  
system and whether or not they are enabled. I suppose that it is  
possible that either the main RHEL binary repo is not configured on  
your system, it is not enabled or perhaps your system is being  
prevented from accessing it. You may have to run that command as 'root'.

An alternative, which has some risk, is to use the CentOS yum repos,  
which are supposed to be binary compatible with RHEL. The risk is that  
if you are in fact paying for RHEL support to RH, I would be hesitant  
to mix and match, if there is any risk of complications in the support  
contract.

Not having the 'devel' versions of the various RPMs will at some point  
cause you problems when installing source packages from CRAN.

A lot of the important details here are going to be dependent upon how  
you installed RHEL and whether or not there is a paid support contract  
in place for your installation.  If you have a SysAdmin that installed  
RHEL for you, he or she would be of help in resolving this.

HTH,

Marc

        
On Nov 13, 2009, at 2:52 PM, Christos Hatzis wrote:

        

            

      
      
      
    

        
http://download.fedora.redhat.com/pub/epel/5/x86_64/epel-release-5-3.noarch

            

      
      
      
    

  
  


  


      

    

    
3 days later

    

      
      

        


  

        

      Christos Hatzis
    

    

      
      #
    

  


  

      
After registering with the RHN, su -c 'yum install R' worked fine.
I now have a working version of R:

            

      
      
      
    

        
R version 2.9.2 (2009-08-24)
x86_64-redhat-linux-gnu

Marc, you mentioned there is a 2.10 available at
 
  http://koji.fedoraproject.org/koji/packageinfo?packageID=1230

Is there an easy way to install that or I'll have to wait until it makes
it to the RHEL repos.

Thank you again.
-Christos

        
On Fri, 2009-11-13 at 17:47 -0500, Christos Hatzis wrote:

            

      
      
      
    

        

      
      
    

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Marc Schwartz
    

    

      
      #
    

  


  

      
Hi Christos,

The R 2.10.0 RPMs will be in the EPEL testing repo until the so-called  
Bodhi system has sufficient positive Karma to move them to release.  
You can see the current status here:

   https://admin.fedoraproject.org/updates/EL-5/FEDORA-EPEL-2009-0809

If you have the EPEL yum repo configuration set up to support the EPEL  
testing repo, which I believe is the case by default, you just need to  
enable that repo, as it should be disabled by default.

Bear in mind that if you are in a production environment, this is a  
testing release and may have problems as with any pre-release  
software. Those problems at this point are more likely in the RPM  
packaging of R, rather than in R itself. I am also presuming that the  
EPEL package is of 2.10.0 initial release and not of a subsequent  
patch release, if you tend to use them (I do on OSX).

Thus, if you elect to proceed, you should be able to use:

su -c "--enablerepo=epel-testing yum update R"

You may want to use the 'yum repolist' command again just to be sure  
of the correct name for the EPEL testing repo, which would be in the  
output of that command.

If you do decide to proceed, I would recommend that after some  
testing, you return to Bodhi to offer your comments and a bump in  
Karma if you do not identify any problems. Getting sufficient Karma is  
required to move the application to a stable release repo and is part  
of the peer review process for Fedora/RHEL-EPEL RPMs.

HTH,

Marc

        
On Nov 17, 2009, at 10:21 AM, Christos Hatzis wrote:

        

            

      
      
      
    

        

      
      
    

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Marc Schwartz
    

    

      
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Sorry, correction on the command below:

   su -c "yum --enablerepo=epel-testing update R"

Time for more coffee...

Marc

        
On Nov 17, 2009, at 10:47 AM, Marc Schwartz wrote:

        

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Christos Hatzis
    

    

      
      #
    

  


  

      
Thanks for all your help, Marc.

This is like a new ecosystem for me, living in the Windows world for too
many years, but will eventually feel like home.  My memories on Unix are
from the Apollo/Domain systems and the Cray-1 and X-MP systems back in grad
school.  Linux is nothing like that, but then again Windows 3.0 was the name
of the game back then. It is really amazing the sophistication and volume of
Linux resources that are available out there. 

-Christos

-----Original Message-----
From: r-sig-fedora-bounces at r-project.org
[mailto:r-sig-fedora-bounces at r-project.org] On Behalf Of Marc Schwartz
Sent: Tuesday, November 17, 2009 11:54 AM
To: Marc Schwartz
Cc: r-sig-fedora at r-project.org; chatzis-rhel at nuverabio.com
Subject: Re: [R-sig-Fedora] Installing R on RedHat EL 5

Sorry, correction on the command below:

   su -c "yum --enablerepo=epel-testing update R"

Time for more coffee...

Marc

        
On Nov 17, 2009, at 10:47 AM, Marc Schwartz wrote:

        

            

      
      
      
    

        
http://download.fedora.redhat.com/pub/epel/5/x86_64/epel-release-5-3.noarch

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

        
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