<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 href="http://www.gtlib.gatech.edu">www.gtlib.gatech.edu</a><br> * epel: <a href="http://www.gtlib.gatech.edu">www.gtlib.gatech.edu</a><br> * extras: <a href="http://www.gtlib.gatech.edu">www.gtlib.gatech.edu</a><br>
* updates: <a href="http://mirror.itc.virginia.edu">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 - $basearch<br>
#baseurl=<a href="http://download.fedoraproject.org/pub/epel/6/$basearch">http://download.fedoraproject.org/pub/epel/6/$basearch</a><br>mirrorlist=<a href="https://mirrors.fedoraproject.org/metalink?repo=epel-6&arch=$basearch">https://mirrors.fedoraproject.org/metalink?repo=epel-6&arch=$basearch</a><br>
failovermethod=priority<br>enabled=0<br>#enabled=1<br>gpgcheck=1<br>gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-EPEL-6<br><br><br><br></div>Did a yum clean all, .. yum install LONCAPA-prerequisites gives the following messages. I guess there are packages that are not needed but somehow got install?? <br>
<br><br><br><div>]$ 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 href="http://www.gtlib.gatech.edu">www.gtlib.gatech.edu</a><br> * extras: <a href="http://mirror.5ninesolutions.com">mirror.5ninesolutions.com</a><br> * updates: <a href="http://centos.mirrors.tds.net">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 href="http://2.13.0-1.centos6.lc">2.13.0-1.centos6.lc</a> will be installed<br>
--> Processing Dependency: R-devel = <a href="http://2.13.0-1.centos6.lc">2.13.0-1.centos6.lc</a> for package: R-2.13.0-1.centos6.lc.x86_64<br>--> Processing Dependency: libRmath-devel = <a href="http://2.13.0-1.centos6.lc">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 href="http://3.7.0-0.centos6.lc">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 href="http://1.1.8-0.centos6.lc">1.1.8-0.centos6.lc</a> will be installed<br>---> Package R-alr3.x86_64 0:<a href="http://1.1.12-0.centos6.lc">1.1.12-0.centos6.lc</a> will be installed<br>
---> Package R-car.x86_64 0:<a href="http://1.2.16-0.centos6.lc">1.2.16-0.centos6.lc</a> will be installed<br>---> Package R-leaps.x86_64 0:<a href="http://2.9-0.centos6.lc">2.9-0.centos6.lc</a> will be installed<br>
---> Package R-lmtest.x86_64 0:<a href="http://0.9.26-0.centos6.lc">0.9.26-0.centos6.lc</a> will be installed<br>---> Package R-phpSerialize.x86_64 0:<a href="http://0.8.1-0.centos6.lc">0.8.1-0.centos6.lc</a> will be installed<br>
---> Package R-qAnalyst.x86_64 0:<a href="http://0.6.0-0.centos6.lc">0.6.0-0.centos6.lc</a> will be installed<br>---> Package R-quadprog.x86_64 0:<a href="http://1.4.12-0.centos6.lc">1.4.12-0.centos6.lc</a> will be installed<br>
---> Package R-zoo.x86_64 0:<a href="http://1.6.2-0.centos6.lc">1.6.2-0.centos6.lc</a> will be installed<br>--> Running transaction check<br>---> Package R.x86_64 0:<a href="http://2.13.0-1.centos6.lc">2.13.0-1.centos6.lc</a> will be installed<br>
--> Processing Dependency: libRmath-devel = <a href="http://2.13.0-1.centos6.lc">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 href="http://2.13.0-1.centos6.lc">2.13.0-1.centos6.lc</a> will be installed<br>
---> Package R-devel.x86_64 0:<a href="http://2.13.0-1.centos6.lc">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 href="http://2.13.0-1.centos6.lc">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 href="http://2.13.0-1.centos6.lc">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 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 class="im HOEnZb"><br>
<br>
Stuart Raeburn<br>
LON-CAPA Academic Consortium<br>
<br>
<br>
<br>
</div><div class="HOEnZb"><div class="h5">Quoting "H. K. Ng" <<a href="mailto:hkng@fsu.edu">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 href="mailto:todd.ruskell@gmail.com">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 href="mailto:raeburn@msu.edu">raeburn@msu.edu</a>> wrote:<br>
>><br>
>>> Todd,<br>
>>><br>
>>> My guess is that you have included the EPEL repo (<br>
>>> <a 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 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 href="mailto:todd.ruskell@gmail.com">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>
>>> <a href="mailto:LON-CAPA-admin@mail.lon-capa.org">LON-CAPA-admin@mail.lon-capa.org</a><br>
>>> <a href="http://mail.lon-capa.org/mailman/listinfo/lon-capa-admin" target="_blank">http://mail.lon-capa.org/mailman/listinfo/lon-capa-admin</a><br>
<br>
<br>
_______________________________________________<br>
LON-CAPA-admin mailing list<br>
<a href="mailto:LON-CAPA-admin@mail.lon-capa.org">LON-CAPA-admin@mail.lon-capa.org</a><br>
<a href="http://mail.lon-capa.org/mailman/listinfo/lon-capa-admin" target="_blank">http://mail.lon-capa.org/mailman/listinfo/lon-capa-admin</a><br>
<br>
<br>
</div></div></blockquote></div><br></div>