[LON-CAPA-admin] Update difficulties

[Stuart Raeburn]

Hi,

To disable the epel repo, and/or eliminate the R conflicts ...


1. Locate the repos currently enabled

yum repolist enabled


2. Use a text editor to add:

enabled=0

to the epel.repo file(s) in /etc/yum.repos.d


3. Then do:

yum clean all


4. If you still have issues, find out if R-core is installed using:

rpm -q R-core

and use:

yum remove R-core

(assuming R-core is installed; all the R packages and the  
LONCAPA-prerequisites rpm will be removed).

and then do:

yum install LONCAPA-prerequisites


Stuart Raeburn
LON-CAPA Academic Consortium



Quoting "H. K. Ng" <hkng at fsu.edu>:

> Hi,
>
> I have the same problem on the development server. I tried to follow
> Stuart's instructions but is not successful. I cannot get to reinstall
> LONCAPA-prerequisites (step (c)). I must not have disable epel properly.
> Any suggestion how to fix the problem?
>
> Thanks,
> -hk
>
> On Thu, Jun 19, 2014 at 10:39 PM, Todd Ruskell <todd.ruskell at gmail.com>
> wrote:
>
>>  Good call, Stuart.  This was exactly it.  As always, thanks for the help
>> and your quick response.
>>
>>  Todd
>>
>>
>> On Thu, Jun 19, 2014 at 12:25 PM, Stuart Raeburn <raeburn at msu.edu> wrote:
>>
>>> Todd,
>>>
>>> My guess is that you have included the EPEL repo (
>>> http://dl.fedoraproject.org/pub/epel/5/) in your enabled repos.
>>>
>>> The version of R available from EPEL 5 is R-3.1.0.el5, but the LON-CAPA
>>> CentOS 5 repository (http://install.loncapa.org) has R-2.13.0-1.el5.
>>>
>>> Packages such as R-quadprog available from the LON-CAPA CentOS 5 repo
>>> were built against this older version of R.
>>>
>>> When time allows (in the near future) I will look into building updated
>>> R-* packages against R-3.1.0, and testing with LON-CAPA 2.11.0.
>>>
>>> If my diagnosis is correct, then one solution for you for now would be to:
>>>
>>> (a) temporarily disable use of the epel repo
>>> (b) use:
>>>
>>> yum remove R-core
>>>
>>> to remove R, R-core, and the other R-* packages, as well as the
>>> LONCAPA-prerequisites rpm
>>>
>>> (c) do:
>>> yum install LONCAPA-prerequisites
>>>
>>> to re-install R, R-core etc. and the LONCAPA-prerequisites rpm from the
>>> LON-CAPA CentOS 5 repo
>>>
>>> (d) re-enable the epel repo
>>> (e) temporarily block update of R and R-core by adding:
>>>
>>> exclude=R,R-core
>>>
>>> to /etc/yum.conf
>>>
>>> Once I have updated the LON-CAPA CentOS repo with newer R-* packages
>>> built against R-3.1.0 you should remove the line: exclude=R,R-core
>>>
>>>
>>> Stuart Raeburn
>>> LON-CAPA Academic Consortium
>>>
>>>
>>>
>>> Quoting Todd Ruskell <todd.ruskell at gmail.com>:
>>>
>>>  When trying to patch our machines, they fail with "Missing Dependency:
>>>> libRblas.so is needed by package R-quadprog-1.4.12-0.centos5.lc.i386
>>>> (loncapa-updates-basearch)"
>>>>
>>>> If you look for the library it's there, but it seems there's something
>>>> wrong with either the yum database or the package itself. Cleaning caches
>>>> doesn't help. Any ideas?
>>>>
>>>> Thanks,
>>>> Todd
>>>>
>>>>
>>>  _______________________________________________
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