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<div class="moz-cite-prefix">Some how your epel repo is enabled
again...!? and is causing conflicts with loncapa-repository. Try
Stuart receipt again + yum remove libRmath(-devel).<br>
<br>
The exclude line could go into the epel repo, but you may find
other problems due to dependencies.<br>
<br>
Eduardo<br>
<br>
On 06/30/2014 03:16 PM, H. K. Ng wrote:<br>
</div>
<blockquote
cite="mid:CAKgMM9jZZfwqhHxKU0EPr2jPWStdanmy1MnAKi5aUHgi_xt4DA@mail.gmail.com"
type="cite">
<div dir="ltr">
<div>Thanks Juan, that did the trick for installing
LONCAPA-prerequisites. However, when I did a yum update, it
gives the following. I did add <br>
<br>
</div>
exclude=R,R-core to yum.conf?? Maybe, the line is in the wrong
location?? Thanks, -hk<br>
<br>
<br>
<div><br>
Loaded plugins: fastestmirror, refresh-packagekit, security<br>
Repository loncapa-testing-basearch is listed more than once
in the configuration<br>
Repository loncapa-testing-noarch is listed more than once in
the configuration<br>
Loading mirror speeds from cached hostfile<br>
epel/metalink
| 9.8 kB 00:00 <br>
* base: <a moz-do-not-send="true"
href="http://reflector.westga.edu">reflector.westga.edu</a><br>
----------This >>> * epel: <a moz-do-not-send="true"
href="http://www.gtlib.gatech.edu">www.gtlib.gatech.edu</a><br>
* extras: <a moz-do-not-send="true"
href="http://mirror.5ninesolutions.com">mirror.5ninesolutions.com</a><br>
* updates: <a moz-do-not-send="true"
href="http://centos.mirrors.tds.net">centos.mirrors.tds.net</a><br>
base
| 3.7 kB 00:00 <br>
epel
| 4.4 kB 00:00 <br>
extras
| 3.4 kB 00:00 <br>
loncapa-testing-basearch
| 951 B 00:00 <br>
loncapa-testing-noarch
| 951 B 00:00 <br>
loncapa-updates-basearch
| 951 B 00:00 <br>
loncapa-updates-noarch
| 951 B 00:00 <br>
updates
| 3.4 kB 00:00 <br>
Setting up Update Process<br>
Resolving Dependencies<br>
--> Running transaction check<br>
---> Package R.x86_64 0:<a moz-do-not-send="true"
href="http://2.13.0-1.centos6.lc">2.13.0-1.centos6.lc</a>
will be updated<br>
---> Package R.x86_64 0:3.1.0-5.el6 will be an update<br>
--> Processing Dependency: R-java = 3.1.0-5.el6 for
package: R-3.1.0-5.el6.x86_64<br>
---> Package R-car.x86_64 0:<a moz-do-not-send="true"
href="http://1.2.16-0.centos6.lc">1.2.16-0.centos6.lc</a>
will be updated<br>
---> Package R-car.noarch 0:2.0.16-1.el6 will be an update<br>
---> Package R-core.x86_64 0:<a moz-do-not-send="true"
href="http://2.13.0-1.centos6.lc">2.13.0-1.centos6.lc</a>
will be updated<br>
--> Processing Dependency: libRblas.so()(64bit) for
package: R-quadprog-1.4.12-0.centos6.lc.x86_64<br>
---> Package R-core.x86_64 0:3.1.0-5.el6 will be an update<br>
---> Package R-devel.x86_64 0:<a moz-do-not-send="true"
href="http://2.13.0-1.centos6.lc">2.13.0-1.centos6.lc</a>
will be updated<br>
---> Package R-devel.x86_64 0:3.1.0-5.el6 will be an update<br>
--> Processing Dependency: R-java-devel = 3.1.0-5.el6 for
package: R-devel-3.1.0-5.el6.x86_64<br>
--> Processing Dependency: R-core-devel = 3.1.0-5.el6 for
package: R-devel-3.1.0-5.el6.x86_64<br>
---> Package R-lmtest.x86_64 0:<a moz-do-not-send="true"
href="http://0.9.26-0.centos6.lc">0.9.26-0.centos6.lc</a>
will be updated<br>
---> Package R-lmtest.x86_64 0:0.9.30-1.el6 will be an
update<br>
---> Package R-zoo.x86_64 0:<a moz-do-not-send="true"
href="http://1.6.2-0.centos6.lc">1.6.2-0.centos6.lc</a> will
be updated<br>
---> Package R-zoo.x86_64 0:1.7.9-1.el6 will be an update<br>
---> Package epel-release.noarch 0:6-5 will be updated<br>
---> Package epel-release.noarch 0:6-8 will be an update<br>
---> Package libRmath.x86_64 0:<a moz-do-not-send="true"
href="http://2.13.0-1.centos6.lc">2.13.0-1.centos6.lc</a>
will be updated<br>
---> Package libRmath.x86_64 0:3.1.0-5.el6 will be an
update<br>
---> Package libRmath-devel.x86_64 0:<a
moz-do-not-send="true" href="http://2.13.0-1.centos6.lc">2.13.0-1.centos6.lc</a>
will be updated<br>
---> Package libRmath-devel.x86_64 0:3.1.0-5.el6 will be an
update<br>
--> Running transaction check<br>
---> Package R-core.x86_64 0:<a moz-do-not-send="true"
href="http://2.13.0-1.centos6.lc">2.13.0-1.centos6.lc</a>
will be updated<br>
--> Processing Dependency: libRblas.so()(64bit) for
package: R-quadprog-1.4.12-0.centos6.lc.x86_64<br>
---> Package R-core-devel.x86_64 0:3.1.0-5.el6 will be
installed<br>
---> Package R-java.x86_64 0:3.1.0-5.el6 will be installed<br>
---> Package R-java-devel.x86_64 0:3.1.0-5.el6 will be
installed<br>
--> Finished Dependency Resolution<br>
Error: Package: R-quadprog-1.4.12-0.centos6.lc.x86_64
(@loncapa-updates-basearch)<br>
Requires: libRblas.so()(64bit)<br>
Removing: R-core-2.13.0-1.centos6.lc.x86_64
(@loncapa-updates-basearch)<br>
libRblas.so()(64bit)<br>
Updated By: R-core-3.1.0-5.el6.x86_64 (epel)<br>
Not found<br>
You could try using --skip-broken to work around the problem<br>
You could try running: rpm -Va --nofiles --nodigest<br>
<br>
<div class="gmail_extra"><br clear="all">
<div>
</div>
<br>
<br>
<div class="gmail_quote">On Mon, Jun 30, 2014 at 2:53 PM,
Juan Eduardo Ramirez <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:eduardo@charma.uprm.edu" target="_blank">eduardo@charma.uprm.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div>Looks like you have a leftover from epel
(libRmath-devel-3.1.0-5)<br>
Perhaps <br>
yum remove libRmath-devel<br>
do the trick?<span class="HOEnZb"><font
color="#888888"><br>
<br>
Eduardo</font></span>
<div>
<div class="h5"><br>
<br>
On 06/30/2014 02:41 PM, H. K. Ng wrote:<br>
</div>
</div>
</div>
<div>
<div class="h5">
<blockquote type="cite">
<div dir="ltr">
<div>
<div>
<div>Thanks Stuart,<br>
<br>
</div>
Still have some problems. This is what
shows up for yum repolist enabled.<br>
<br>
Loaded plugins: fastestmirror,
refresh-packagekit, security<br>
Loading mirror speeds from cached hostfile<br>
* base: <a moz-do-not-send="true"
href="http://www.gtlib.gatech.edu"
target="_blank">www.gtlib.gatech.edu</a><br>
* epel: <a moz-do-not-send="true"
href="http://www.gtlib.gatech.edu"
target="_blank">www.gtlib.gatech.edu</a><br>
* extras: <a moz-do-not-send="true"
href="http://www.gtlib.gatech.edu"
target="_blank">www.gtlib.gatech.edu</a><br>
* updates: <a moz-do-not-send="true"
href="http://mirror.itc.virginia.edu"
target="_blank">mirror.itc.virginia.edu</a><br>
repo id repo
name
status<br>
base CentOS-6 -
Base
6,367<br>
epel Extra Packages
for Enterprise Linux 6 - x86_64 10,962<br>
extras CentOS-6 -
Extras
14<br>
loncapa-testing-basearch Centos 6
LON-CAPA x86_64
Testing 0<br>
loncapa-testing-noarch Centos 6
LON-CAPA noarch
Testing 0<br>
loncapa-updates-basearch CentOS 6
LON-CAPA x86_64 Updates
46<br>
loncapa-updates-noarch CentOS 6
LON-CAPA noarch Updates
17<br>
updates CentOS-6 -
Updates
1,103<br>
repolist: 18,509<br>
<br>
</div>
<br>
<br>
2. add enabled=0 to epel.repo<br>
<br>
[epel]<br>
name=Extra Packages for Enterprise Linux 6 -
$basearch<br>
#baseurl=<a moz-do-not-send="true"
href="http://download.fedoraproject.org/pub/epel/6/$basearch"
target="_blank">http://download.fedoraproject.org/pub/epel/6/$basearch</a><br>
mirrorlist=<a moz-do-not-send="true"
href="https://mirrors.fedoraproject.org/metalink?repo=epel-6&arch=$basearch"
target="_blank">https://mirrors.fedoraproject.org/metalink?repo=epel-6&arch=$basearch</a><br>
failovermethod=priority<br>
enabled=0<br>
#enabled=1<br>
gpgcheck=1<br>
gpgkey=<a moz-do-not-send="true">file:///etc/pki/rpm-gpg/RPM-GPG-KEY-EPEL-6</a><br>
<br>
<br>
<br>
</div>
Did a yum clean all, .. yum install
LONCAPA-prerequisites gives the following
messages. I guess there are packages that are
not needed but somehow got install??
<br>
<br>
<br>
<br>
<div>]$ sudo yum install LONCAPA-prerequisites<br>
Loaded plugins: fastestmirror,
refresh-packagekit, security<br>
Repository loncapa-testing-basearch is
listed more than once in the configuration<br>
Repository loncapa-testing-noarch is listed
more than once in the configuration<br>
Loading mirror speeds from cached hostfile<br>
* base: <a moz-do-not-send="true"
href="http://www.gtlib.gatech.edu"
target="_blank">www.gtlib.gatech.edu</a><br>
* extras: <a moz-do-not-send="true"
href="http://mirror.5ninesolutions.com"
target="_blank">mirror.5ninesolutions.com</a><br>
* updates: <a moz-do-not-send="true"
href="http://centos.mirrors.tds.net"
target="_blank">centos.mirrors.tds.net</a><br>
Setting up Install Process<br>
Resolving Dependencies<br>
--> Running transaction check<br>
---> Package LONCAPA-prerequisites.x86_64
0:1-23.centos6 will be installed<br>
--> Processing Dependency: R-lmtest for
package:
LONCAPA-prerequisites-1-23.centos6.x86_64<br>
--> Processing Dependency: R-leaps for
package:
LONCAPA-prerequisites-1-23.centos6.x86_64<br>
--> Processing Dependency: R-qAnalyst for
package:
LONCAPA-prerequisites-1-23.centos6.x86_64<br>
--> Processing Dependency: R-Hmisc for
package:
LONCAPA-prerequisites-1-23.centos6.x86_64<br>
--> Processing Dependency: R-car for
package:
LONCAPA-prerequisites-1-23.centos6.x86_64<br>
--> Processing Dependency: R-quadprog for
package:
LONCAPA-prerequisites-1-23.centos6.x86_64<br>
--> Processing Dependency: R-zoo for
package:
LONCAPA-prerequisites-1-23.centos6.x86_64<br>
--> Processing Dependency: R-phpSerialize
for package:
LONCAPA-prerequisites-1-23.centos6.x86_64<br>
--> Processing Dependency: R-SuppDists
for package:
LONCAPA-prerequisites-1-23.centos6.x86_64<br>
--> Processing Dependency: R-alr3 for
package:
LONCAPA-prerequisites-1-23.centos6.x86_64<br>
--> Processing Dependency: R for package:
LONCAPA-prerequisites-1-23.centos6.x86_64<br>
--> Running transaction check<br>
---> Package R.x86_64 0:<a
moz-do-not-send="true"
href="http://2.13.0-1.centos6.lc"
target="_blank">2.13.0-1.centos6.lc</a>
will be installed<br>
--> Processing Dependency: R-devel = <a
moz-do-not-send="true"
href="http://2.13.0-1.centos6.lc"
target="_blank">
2.13.0-1.centos6.lc</a> for package:
R-2.13.0-1.centos6.lc.x86_64<br>
--> Processing Dependency: libRmath-devel
= <a moz-do-not-send="true"
href="http://2.13.0-1.centos6.lc"
target="_blank">
2.13.0-1.centos6.lc</a> for package:
R-2.13.0-1.centos6.lc.x86_64<br>
---> Package R-Hmisc.x86_64 0:<a
moz-do-not-send="true"
href="http://3.7.0-0.centos6.lc"
target="_blank">3.7.0-0.centos6.lc</a>
will be installed<br>
--> Processing Dependency: R-core for
package: R-Hmisc-3.7.0-0.centos6.lc.x86_64<br>
--> Processing Dependency:
libR.so()(64bit) for package:
R-Hmisc-3.7.0-0.centos6.lc.x86_64<br>
---> Package R-SuppDists.x86_64 0:<a
moz-do-not-send="true"
href="http://1.1.8-0.centos6.lc"
target="_blank">1.1.8-0.centos6.lc</a>
will be installed<br>
---> Package R-alr3.x86_64 0:<a
moz-do-not-send="true"
href="http://1.1.12-0.centos6.lc"
target="_blank">1.1.12-0.centos6.lc</a>
will be installed<br>
---> Package R-car.x86_64 0:<a
moz-do-not-send="true"
href="http://1.2.16-0.centos6.lc"
target="_blank">1.2.16-0.centos6.lc</a>
will be installed<br>
---> Package R-leaps.x86_64 0:<a
moz-do-not-send="true"
href="http://2.9-0.centos6.lc"
target="_blank">2.9-0.centos6.lc</a> will
be installed<br>
---> Package R-lmtest.x86_64 0:<a
moz-do-not-send="true"
href="http://0.9.26-0.centos6.lc"
target="_blank">0.9.26-0.centos6.lc</a>
will be installed<br>
---> Package R-phpSerialize.x86_64 0:<a
moz-do-not-send="true"
href="http://0.8.1-0.centos6.lc"
target="_blank">0.8.1-0.centos6.lc</a>
will be installed<br>
---> Package R-qAnalyst.x86_64 0:<a
moz-do-not-send="true"
href="http://0.6.0-0.centos6.lc"
target="_blank">0.6.0-0.centos6.lc</a>
will be installed<br>
---> Package R-quadprog.x86_64 0:<a
moz-do-not-send="true"
href="http://1.4.12-0.centos6.lc"
target="_blank">1.4.12-0.centos6.lc</a>
will be installed<br>
---> Package R-zoo.x86_64 0:<a
moz-do-not-send="true"
href="http://1.6.2-0.centos6.lc"
target="_blank">1.6.2-0.centos6.lc</a>
will be installed<br>
--> Running transaction check<br>
---> Package R.x86_64 0:<a
moz-do-not-send="true"
href="http://2.13.0-1.centos6.lc"
target="_blank">2.13.0-1.centos6.lc</a>
will be installed<br>
--> Processing Dependency: libRmath-devel
= <a moz-do-not-send="true"
href="http://2.13.0-1.centos6.lc"
target="_blank">
2.13.0-1.centos6.lc</a> for package:
R-2.13.0-1.centos6.lc.x86_64<br>
---> Package R-core.x86_64 0:<a
moz-do-not-send="true"
href="http://2.13.0-1.centos6.lc"
target="_blank">2.13.0-1.centos6.lc</a>
will be installed<br>
---> Package R-devel.x86_64 0:<a
moz-do-not-send="true"
href="http://2.13.0-1.centos6.lc"
target="_blank">2.13.0-1.centos6.lc</a>
will be installed<br>
--> Finished Dependency Resolution<br>
Error: Package: R-2.13.0-1.centos6.lc.x86_64
(loncapa-updates-basearch)<br>
Requires: libRmath-devel = <a
moz-do-not-send="true"
href="http://2.13.0-1.centos6.lc"
target="_blank">
2.13.0-1.centos6.lc</a><br>
Installed:
libRmath-devel-3.1.0-5.el6.x86_64 (@epel)<br>
libRmath-devel = 3.1.0-5.el6<br>
Available:
libRmath-devel-2.13.0-1.centos6.lc.x86_64
(loncapa-updates-basearch)<br>
libRmath-devel = <a
moz-do-not-send="true"
href="http://2.13.0-1.centos6.lc"
target="_blank">
2.13.0-1.centos6.lc</a><br>
You could try using --skip-broken to work
around the problem<br>
You could try running: rpm -Va --nofiles
--nodigest<br>
<br>
</div>
</div>
<div class="gmail_extra"><br clear="all">
<div>
<div dir="ltr">
<div>
<div>
<div>H. K. Ng<br>
</div>
Associate Professor of Physics<br>
</div>
<div>Department of Physics<br>
</div>
Florida State University<br>
</div>
Tallahassee, FL 32306-4350<br>
</div>
</div>
<br>
<br>
<div class="gmail_quote">On Mon, Jun 30, 2014
at 2:24 PM, Stuart Raeburn <span dir="ltr">
<<a moz-do-not-send="true"
href="mailto:raeburn@msu.edu"
target="_blank">raeburn@msu.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote"
style="margin:0 0 0 .8ex;border-left:1px
#ccc solid;padding-left:1ex">
Hi,<br>
<br>
To disable the epel repo, and/or eliminate
the R conflicts ...<br>
<br>
<br>
1. Locate the repos currently enabled<br>
<br>
yum repolist enabled<br>
<br>
<br>
2. Use a text editor to add:<br>
<br>
enabled=0<br>
<br>
to the epel.repo file(s) in
/etc/yum.repos.d<br>
<br>
<br>
3. Then do:<br>
<br>
yum clean all<br>
<br>
<br>
4. If you still have issues, find out if
R-core is installed using:<br>
<br>
rpm -q R-core<br>
<br>
and use:<br>
<br>
yum remove R-core<br>
<br>
(assuming R-core is installed; all the R
packages and the<br>
LONCAPA-prerequisites rpm will be
removed).<br>
<br>
and then do:<br>
<br>
yum install LONCAPA-prerequisites<br>
<div><br>
<br>
Stuart Raeburn<br>
LON-CAPA Academic Consortium<br>
<br>
<br>
<br>
</div>
<div>
<div>Quoting "H. K. Ng" <<a
moz-do-not-send="true"
href="mailto:hkng@fsu.edu"
target="_blank">hkng@fsu.edu</a>>:<br>
<br>
> Hi,<br>
><br>
> I have the same problem on the
development server. I tried to follow<br>
> Stuart's instructions but is not
successful. I cannot get to reinstall<br>
> LONCAPA-prerequisites (step (c)).
I must not have disable epel properly.<br>
> Any suggestion how to fix the
problem?<br>
><br>
> Thanks,<br>
> -hk<br>
><br>
> On Thu, Jun 19, 2014 at 10:39 PM,
Todd Ruskell <<a
moz-do-not-send="true"
href="mailto:todd.ruskell@gmail.com"
target="_blank">todd.ruskell@gmail.com</a>><br>
> wrote:<br>
><br>
>> Good call, Stuart. This was
exactly it. As always, thanks for the
help<br>
>> and your quick response.<br>
>><br>
>> Todd<br>
>><br>
>><br>
>> On Thu, Jun 19, 2014 at 12:25
PM, Stuart Raeburn <<a
moz-do-not-send="true"
href="mailto:raeburn@msu.edu"
target="_blank">raeburn@msu.edu</a>>
wrote:<br>
>><br>
>>> Todd,<br>
>>><br>
>>> My guess is that you have
included the EPEL repo (<br>
>>> <a
moz-do-not-send="true"
href="http://dl.fedoraproject.org/pub/epel/5/"
target="_blank">
http://dl.fedoraproject.org/pub/epel/5/</a>) in your enabled repos.<br>
>>><br>
>>> The version of R
available from EPEL 5 is R-3.1.0.el5,
but the LON-CAPA<br>
>>> CentOS 5 repository (<a
moz-do-not-send="true"
href="http://install.loncapa.org"
target="_blank">http://install.loncapa.org</a>)
has R-2.13.0-1.el5.<br>
>>><br>
>>> Packages such as
R-quadprog available from the LON-CAPA
CentOS 5 repo<br>
>>> were built against this
older version of R.<br>
>>><br>
>>> When time allows (in the
near future) I will look into building
updated<br>
>>> R-* packages against
R-3.1.0, and testing with LON-CAPA
2.11.0.<br>
>>><br>
>>> If my diagnosis is
correct, then one solution for you for
now would be to:<br>
>>><br>
>>> (a) temporarily disable
use of the epel repo<br>
>>> (b) use:<br>
>>><br>
>>> yum remove R-core<br>
>>><br>
>>> to remove R, R-core, and
the other R-* packages, as well as the<br>
>>> LONCAPA-prerequisites rpm<br>
>>><br>
>>> (c) do:<br>
>>> yum install
LONCAPA-prerequisites<br>
>>><br>
>>> to re-install R, R-core
etc. and the LONCAPA-prerequisites rpm
from the<br>
>>> LON-CAPA CentOS 5 repo<br>
>>><br>
>>> (d) re-enable the epel
repo<br>
>>> (e) temporarily block
update of R and R-core by adding:<br>
>>><br>
>>> exclude=R,R-core<br>
>>><br>
>>> to /etc/yum.conf<br>
>>><br>
>>> Once I have updated the
LON-CAPA CentOS repo with newer R-*
packages<br>
>>> built against R-3.1.0 you
should remove the line:
exclude=R,R-core<br>
>>><br>
>>><br>
>>> Stuart Raeburn<br>
>>> LON-CAPA Academic
Consortium<br>
>>><br>
>>><br>
>>><br>
>>> Quoting Todd Ruskell <<a
moz-do-not-send="true"
href="mailto:todd.ruskell@gmail.com"
target="_blank">todd.ruskell@gmail.com</a>>:<br>
>>><br>
>>> When trying to patch our
machines, they fail with "Missing
Dependency:<br>
>>>> libRblas.so is needed
by package
R-quadprog-1.4.12-0.centos5.lc.i386<br>
>>>>
(loncapa-updates-basearch)"<br>
>>>><br>
>>>> If you look for the
library it's there, but it seems
there's something<br>
>>>> wrong with either the
yum database or the package itself.
Cleaning caches<br>
>>>> doesn't help. Any
ideas?<br>
>>>><br>
>>>> Thanks,<br>
>>>> Todd<br>
>>>><br>
>>>><br>
>>>
_______________________________________________<br>
>>> LON-CAPA-admin mailing
list<br>
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moz-do-not-send="true"
href="mailto:LON-CAPA-admin@mail.lon-capa.org"
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target="_blank">
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