[LON-CAPA-admin] Update difficulties
H. K. Ng
hkng at fsu.edu
Mon Jun 30 15:16:12 EDT 2014
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
* epel: www.gtlib.gatech.edu
* extras: mirror.5ninesolutions.com
* updates: 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 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 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 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 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 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 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 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 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 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> 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
> * 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
>>
>>
>> _______________________________________________
>> 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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