[LON-CAPA-admin] Update difficulties
Juan Eduardo Ramirez
eduardo at charma.uprm.edu
Mon Jun 30 16:00:21 EDT 2014
Some how your epel repo is enabled again...!? and is causing conflicts
with loncapa-repository. Try Stuart receipt again + yum remove
libRmath(-devel).
The exclude line could go into the epel repo, but you may find other
problems due to dependencies.
Eduardo
On 06/30/2014 03:16 PM, H. K. Ng wrote:
> Thanks Juan, that did the trick for installing LONCAPA-prerequisites.
> However, when I did a yum update, it gives the following. I did add
>
> exclude=R,R-core to yum.conf?? Maybe, the line is in the wrong
> location?? Thanks, -hk
>
>
>
> 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
> epel/metalink | 9.8 kB 00:00
> * base: reflector.westga.edu <http://reflector.westga.edu>
> ----------This >>> * epel: 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>
> base | 3.7 kB 00:00
> epel | 4.4 kB 00:00
> extras | 3.4 kB 00:00
> loncapa-testing-basearch | 951 B 00:00
> loncapa-testing-noarch | 951 B 00:00
> loncapa-updates-basearch | 951 B 00:00
> loncapa-updates-noarch | 951 B 00:00
> updates | 3.4 kB 00:00
> Setting up Update Process
> Resolving Dependencies
> --> Running transaction check
> ---> Package R.x86_64 0:2.13.0-1.centos6.lc
> <http://2.13.0-1.centos6.lc> will be updated
> ---> Package R.x86_64 0:3.1.0-5.el6 will be an update
> --> Processing Dependency: R-java = 3.1.0-5.el6 for package:
> R-3.1.0-5.el6.x86_64
> ---> Package R-car.x86_64 0:1.2.16-0.centos6.lc
> <http://1.2.16-0.centos6.lc> will be updated
> ---> Package R-car.noarch 0:2.0.16-1.el6 will be an update
> ---> Package R-core.x86_64 0:2.13.0-1.centos6.lc
> <http://2.13.0-1.centos6.lc> will be updated
> --> Processing Dependency: libRblas.so()(64bit) for package:
> R-quadprog-1.4.12-0.centos6.lc.x86_64
> ---> Package R-core.x86_64 0:3.1.0-5.el6 will be an update
> ---> Package R-devel.x86_64 0:2.13.0-1.centos6.lc
> <http://2.13.0-1.centos6.lc> will be updated
> ---> Package R-devel.x86_64 0:3.1.0-5.el6 will be an update
> --> Processing Dependency: R-java-devel = 3.1.0-5.el6 for package:
> R-devel-3.1.0-5.el6.x86_64
> --> Processing Dependency: R-core-devel = 3.1.0-5.el6 for package:
> R-devel-3.1.0-5.el6.x86_64
> ---> Package R-lmtest.x86_64 0:0.9.26-0.centos6.lc
> <http://0.9.26-0.centos6.lc> will be updated
> ---> Package R-lmtest.x86_64 0:0.9.30-1.el6 will be an update
> ---> Package R-zoo.x86_64 0:1.6.2-0.centos6.lc
> <http://1.6.2-0.centos6.lc> will be updated
> ---> Package R-zoo.x86_64 0:1.7.9-1.el6 will be an update
> ---> Package epel-release.noarch 0:6-5 will be updated
> ---> Package epel-release.noarch 0:6-8 will be an update
> ---> Package libRmath.x86_64 0:2.13.0-1.centos6.lc
> <http://2.13.0-1.centos6.lc> will be updated
> ---> Package libRmath.x86_64 0:3.1.0-5.el6 will be an update
> ---> Package libRmath-devel.x86_64 0:2.13.0-1.centos6.lc
> <http://2.13.0-1.centos6.lc> will be updated
> ---> Package libRmath-devel.x86_64 0:3.1.0-5.el6 will be an update
> --> Running transaction check
> ---> Package R-core.x86_64 0:2.13.0-1.centos6.lc
> <http://2.13.0-1.centos6.lc> will be updated
> --> Processing Dependency: libRblas.so()(64bit) for package:
> R-quadprog-1.4.12-0.centos6.lc.x86_64
> ---> Package R-core-devel.x86_64 0:3.1.0-5.el6 will be installed
> ---> Package R-java.x86_64 0:3.1.0-5.el6 will be installed
> ---> Package R-java-devel.x86_64 0:3.1.0-5.el6 will be installed
> --> Finished Dependency Resolution
> Error: Package: R-quadprog-1.4.12-0.centos6.lc.x86_64
> (@loncapa-updates-basearch)
> Requires: libRblas.so()(64bit)
> Removing: R-core-2.13.0-1.centos6.lc.x86_64
> (@loncapa-updates-basearch)
> libRblas.so()(64bit)
> Updated By: R-core-3.1.0-5.el6.x86_64 (epel)
> Not found
> You could try using --skip-broken to work around the problem
> You could try running: rpm -Va --nofiles --nodigest
>
>
>
>
> On Mon, Jun 30, 2014 at 2:53 PM, Juan Eduardo Ramirez
> <eduardo at charma.uprm.edu <mailto:eduardo at charma.uprm.edu>> wrote:
>
> 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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>>
>>
>>
>>
>>
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>
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