[LON-CAPA-admin] Update difficulties
H. K. Ng
hkng at fsu.edu
Mon Jun 30 14:41:12 EDT 2014
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
* epel: www.gtlib.gatech.edu
* extras: www.gtlib.gatech.edu
* updates: 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
* extras: mirror.5ninesolutions.com
* updates: 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 will be installed
--> Processing Dependency: R-devel = 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 for
package: R-2.13.0-1.centos6.lc.x86_64
---> Package R-Hmisc.x86_64 0:3.7.0-0.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 will be installed
---> Package R-alr3.x86_64 0:1.1.12-0.centos6.lc will be installed
---> Package R-car.x86_64 0:1.2.16-0.centos6.lc will be installed
---> Package R-leaps.x86_64 0:2.9-0.centos6.lc will be installed
---> Package R-lmtest.x86_64 0:0.9.26-0.centos6.lc will be installed
---> Package R-phpSerialize.x86_64 0:0.8.1-0.centos6.lc will be installed
---> Package R-qAnalyst.x86_64 0:0.6.0-0.centos6.lc will be installed
---> Package R-quadprog.x86_64 0:1.4.12-0.centos6.lc will be installed
---> Package R-zoo.x86_64 0:1.6.2-0.centos6.lc will be installed
--> Running transaction check
---> Package R.x86_64 0:2.13.0-1.centos6.lc will be installed
--> Processing Dependency: libRmath-devel = 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 will be installed
---> Package R-devel.x86_64 0:2.13.0-1.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
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
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> 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>:
>
> > 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
> >>>>
> >>>>
> >>> _______________________________________________
> >>> LON-CAPA-admin mailing list
> >>> LON-CAPA-admin at mail.lon-capa.org
> >>> http://mail.lon-capa.org/mailman/listinfo/lon-capa-admin
>
>
> _______________________________________________
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>
>
>
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