[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
>
>
> _______________________________________________
> 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
>
>
>
>
>
> _______________________________________________
> LON-CAPA-admin mailing list
> LON-CAPA-admin at mail.lon-capa.org
> http://mail.lon-capa.org/mailman/listinfo/lon-capa-admin
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.lon-capa.org/pipermail/lon-capa-admin/attachments/20140630/e04f993b/attachment-0001.html>
More information about the LON-CAPA-admin
mailing list