[R-sig-Fedora] Installing R on RedHat EL 5

Marc Schwartz marc_schwartz at me.com
Tue Nov 17 17:53:55 CET 2009 

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:

> 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:
>
>> After registering with the RHN, su -c 'yum install R' worked fine.
>> I now have a working version of R:
>>
>>> sessionInfo()
>> 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,
>>>
>>> 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:
>>>
>>>> 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:
>>>>> On Nov 13, 2009, at 1:59 PM, Christos Hatzis wrote:
>>>>>
>>>>>> 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
>>>>>
>>>>> 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, Ph.D.
>>>> Nuvera Biosciences
>>>> Woburn, MA 01801
>>>>
>>>
>>> _______________________________________________
>>> R-SIG-Fedora mailing list
>>> R-SIG-Fedora at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-fedora
>>>
>> -- 
>> Christos Hatzis, Ph.D.
>> Nuvera Biosciences
>> Woburn, MA 01801
>>
>
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