[LON-CAPA-admin] Update difficulties

Juan Eduardo Ramirez eduardo at charma.uprm.edu
Mon Jun 30 14:53:00 EDT 2014


Looks like you have a leftover from epel (libRmath-devel-3.1.0-5)
Perhaps
yum remove libRmath-devel
do the trick?

Eduardo

On 06/30/2014 02:41 PM, H. K. Ng wrote:
> Thanks Stuart,
>
> Still have some problems. This is what shows up for yum repolist enabled.
>
> Loaded plugins: fastestmirror, refresh-packagekit, security
> Loading mirror speeds from cached hostfile
>  * base: www.gtlib.gatech.edu <http://www.gtlib.gatech.edu>
>  * epel: www.gtlib.gatech.edu <http://www.gtlib.gatech.edu>
>  * extras: www.gtlib.gatech.edu <http://www.gtlib.gatech.edu>
>  * updates: mirror.itc.virginia.edu <http://mirror.itc.virginia.edu>
> repo id                   repo 
> name                                       status
> base                      CentOS-6 - 
> Base                                  6,367
> epel                      Extra Packages for Enterprise Linux 6 - 
> x86_64  10,962
> extras                    CentOS-6 - 
> Extras                                   14
> loncapa-testing-basearch  Centos 6 LON-CAPA x86_64 
> Testing                     0
> loncapa-testing-noarch    Centos 6 LON-CAPA noarch 
> Testing                     0
> loncapa-updates-basearch  CentOS 6 LON-CAPA x86_64 
> Updates                    46
> loncapa-updates-noarch    CentOS 6 LON-CAPA noarch 
> Updates                    17
> updates                   CentOS-6 - 
> Updates                               1,103
> repolist: 18,509
>
>
>
> 2. add enabled=0 to epel.repo
>
> [epel]
> name=Extra Packages for Enterprise Linux 6 - $basearch
> #baseurl=http://download.fedoraproject.org/pub/epel/6/$basearch
> mirrorlist=https://mirrors.fedoraproject.org/metalink?repo=epel-6&arch=$basearch
> failovermethod=priority
> enabled=0
> #enabled=1
> gpgcheck=1
> gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-EPEL-6
>
>
>
> Did a yum clean all, .. yum install LONCAPA-prerequisites gives the 
> following messages. I guess there are packages that are not needed but 
> somehow got install??
>
>
>
> ]$ sudo yum install LONCAPA-prerequisites
> Loaded plugins: fastestmirror, refresh-packagekit, security
> Repository loncapa-testing-basearch is listed more than once in the 
> configuration
> Repository loncapa-testing-noarch is listed more than once in the 
> configuration
> Loading mirror speeds from cached hostfile
>  * base: www.gtlib.gatech.edu <http://www.gtlib.gatech.edu>
>  * extras: mirror.5ninesolutions.com <http://mirror.5ninesolutions.com>
>  * updates: centos.mirrors.tds.net <http://centos.mirrors.tds.net>
> Setting up Install Process
> Resolving Dependencies
> --> Running transaction check
> ---> Package LONCAPA-prerequisites.x86_64 0:1-23.centos6 will be installed
> --> Processing Dependency: R-lmtest for package: 
> LONCAPA-prerequisites-1-23.centos6.x86_64
> --> Processing Dependency: R-leaps for package: 
> LONCAPA-prerequisites-1-23.centos6.x86_64
> --> Processing Dependency: R-qAnalyst for package: 
> LONCAPA-prerequisites-1-23.centos6.x86_64
> --> Processing Dependency: R-Hmisc for package: 
> LONCAPA-prerequisites-1-23.centos6.x86_64
> --> Processing Dependency: R-car for package: 
> LONCAPA-prerequisites-1-23.centos6.x86_64
> --> Processing Dependency: R-quadprog for package: 
> LONCAPA-prerequisites-1-23.centos6.x86_64
> --> Processing Dependency: R-zoo for package: 
> LONCAPA-prerequisites-1-23.centos6.x86_64
> --> Processing Dependency: R-phpSerialize for package: 
> LONCAPA-prerequisites-1-23.centos6.x86_64
> --> Processing Dependency: R-SuppDists for package: 
> LONCAPA-prerequisites-1-23.centos6.x86_64
> --> Processing Dependency: R-alr3 for package: 
> LONCAPA-prerequisites-1-23.centos6.x86_64
> --> Processing Dependency: R for package: 
> LONCAPA-prerequisites-1-23.centos6.x86_64
> --> Running transaction check
> ---> Package R.x86_64 0:2.13.0-1.centos6.lc 
> <http://2.13.0-1.centos6.lc> will be installed
> --> Processing Dependency: R-devel = 2.13.0-1.centos6.lc 
> <http://2.13.0-1.centos6.lc> for package: R-2.13.0-1.centos6.lc.x86_64
> --> Processing Dependency: libRmath-devel = 2.13.0-1.centos6.lc 
> <http://2.13.0-1.centos6.lc> for package: R-2.13.0-1.centos6.lc.x86_64
> ---> Package R-Hmisc.x86_64 0:3.7.0-0.centos6.lc 
> <http://3.7.0-0.centos6.lc> will be installed
> --> Processing Dependency: R-core for package: 
> R-Hmisc-3.7.0-0.centos6.lc.x86_64
> --> Processing Dependency: libR.so()(64bit) for package: 
> R-Hmisc-3.7.0-0.centos6.lc.x86_64
> ---> Package R-SuppDists.x86_64 0:1.1.8-0.centos6.lc 
> <http://1.1.8-0.centos6.lc> will be installed
> ---> Package R-alr3.x86_64 0:1.1.12-0.centos6.lc 
> <http://1.1.12-0.centos6.lc> will be installed
> ---> Package R-car.x86_64 0:1.2.16-0.centos6.lc 
> <http://1.2.16-0.centos6.lc> will be installed
> ---> Package R-leaps.x86_64 0:2.9-0.centos6.lc 
> <http://2.9-0.centos6.lc> will be installed
> ---> Package R-lmtest.x86_64 0:0.9.26-0.centos6.lc 
> <http://0.9.26-0.centos6.lc> will be installed
> ---> Package R-phpSerialize.x86_64 0:0.8.1-0.centos6.lc 
> <http://0.8.1-0.centos6.lc> will be installed
> ---> Package R-qAnalyst.x86_64 0:0.6.0-0.centos6.lc 
> <http://0.6.0-0.centos6.lc> will be installed
> ---> Package R-quadprog.x86_64 0:1.4.12-0.centos6.lc 
> <http://1.4.12-0.centos6.lc> will be installed
> ---> Package R-zoo.x86_64 0:1.6.2-0.centos6.lc 
> <http://1.6.2-0.centos6.lc> will be installed
> --> Running transaction check
> ---> Package R.x86_64 0:2.13.0-1.centos6.lc 
> <http://2.13.0-1.centos6.lc> will be installed
> --> Processing Dependency: libRmath-devel = 2.13.0-1.centos6.lc 
> <http://2.13.0-1.centos6.lc> for package: R-2.13.0-1.centos6.lc.x86_64
> ---> Package R-core.x86_64 0:2.13.0-1.centos6.lc 
> <http://2.13.0-1.centos6.lc> will be installed
> ---> Package R-devel.x86_64 0:2.13.0-1.centos6.lc 
> <http://2.13.0-1.centos6.lc> will be installed
> --> Finished Dependency Resolution
> Error: Package: R-2.13.0-1.centos6.lc.x86_64 (loncapa-updates-basearch)
>            Requires: libRmath-devel = 2.13.0-1.centos6.lc 
> <http://2.13.0-1.centos6.lc>
>            Installed: libRmath-devel-3.1.0-5.el6.x86_64 (@epel)
>                libRmath-devel = 3.1.0-5.el6
>            Available: libRmath-devel-2.13.0-1.centos6.lc.x86_64 
> (loncapa-updates-basearch)
>                libRmath-devel = 2.13.0-1.centos6.lc 
> <http://2.13.0-1.centos6.lc>
>  You could try using --skip-broken to work around the problem
>  You could try running: rpm -Va --nofiles --nodigest
>
>
> H. K. Ng
> Associate Professor of Physics
> Department of Physics
> Florida State University
> Tallahassee, FL 32306-4350
>
>
> On Mon, Jun 30, 2014 at 2:24 PM, Stuart Raeburn <raeburn at msu.edu 
> <mailto:raeburn at msu.edu>> wrote:
>
>     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 <mailto: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 <mailto: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 <mailto: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
>     <mailto: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
>     >>>>
>     >>>>
>     >>>  _______________________________________________
>     >>> LON-CAPA-admin mailing list
>     >>> LON-CAPA-admin at mail.lon-capa.org
>     <mailto:LON-CAPA-admin at mail.lon-capa.org>
>     >>> http://mail.lon-capa.org/mailman/listinfo/lon-capa-admin
>
>
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>     <mailto:LON-CAPA-admin at mail.lon-capa.org>
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>
>
>
>
>
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