Login

News

R install of openmx breaks with R update 3.3.2

Posted on
No user picture. rsphadmin Joined: 01/05/2017
Forums
OpenMx Installation
I had the R version of openmx 2.3.1 working on R 3.2 but after the update it no longer will install or update. I was trying to go to 2.6.9, but now not even 2.3.1 will install.
OS RHEL 6
error message attached:
Replied on Thu, 01/05/2017 - 13:06
Picture of user. jpritikin Joined: 05/23/2012

We recommend gcc 5.4. Which version of gcc are you using?
Log in or register to post comments
Replied on Thu, 01/05/2017 - 13:15
No user picture. rsphadmin Joined: 01/05/2017

Using gcc 4.4.7 by default as it is RHEL. There dont seem to be compile time options to pass it to have it use the 4.8.1 gcc I have. I am installing this on a cluster for other users so using the ~/R/Makevars is not an option as users wont have access to root dirs.
Log in or register to post comments
Replied on Thu, 01/05/2017 - 13:33
Picture of user. jpritikin Joined: 05/23/2012

What I did for users here at the VCU cluster is to compile gcc 5.4 from source and use that to compile OpenMx. It's not all that difficult.
Log in or register to post comments
Replied on Thu, 01/05/2017 - 13:41
No user picture. rsphadmin Joined: 01/05/2017

as part of epel I have openmx.x86_64 version 3.7.10 installed already.
This problem is in reference to the R CRAN repository OpenMx install. Which when I downloaded and tried to even do a configure to do a manual compile was not helpful
./configure
Change default C/C++ compiler and default compile flags by editing ~/.R/Makevars
so yes I completely agree that I could download and install a newer version of gcc, but only if I can actually compile the R package with that gcc does this help.
Log in or register to post comments
Replied on Thu, 01/05/2017 - 14:40
Picture of user. jpritikin Joined: 05/23/2012

./configure is not a autoconf style script. It is designed for R CMD INSTALL.

Take a look at http://openmx.ssri.psu.edu/wiki/howto-build-openmx-source-repository?q=wiki/howto-build-openmx-source-repository

Log in or register to post comments
Replied on Thu, 01/05/2017 - 15:15
No user picture. rsphadmin Joined: 01/05/2017

git clone git@github.com:OpenMx/OpenMx.git
Initialized empty Git repository in /OpenMx/.git/
Permission denied (publickey).
fatal: The remote end hung up unexpectedly
Log in or register to post comments
Replied on Thu, 01/05/2017 - 15:21
No user picture. rsphadmin Joined: 01/05/2017

OK i should have thought about it before but I used environmental modules and got it to install but I think this means users will have to load the gcc 4.8.1 module to use openmx within R from now on.
#!/bin/bash
. $MODULESHOME/init/bash
module load compilers/gcc-4.8.1
#now can actuall install of OpenMx
/usr/bin/R --vanilla < /usr/local/src/R_modules/ROpenMx

does this sound correct or once its built it should work without loading gcc 4.8.1?

Log in or register to post comments
Replied on Thu, 01/05/2017 - 15:33
Picture of user. jpritikin Joined: 05/23/2012

There is probably a way to make it work without loading the gcc module, but I couldn't figure it out either. I ended up setting the gcc environment variables as you have done.
Log in or register to post comments
  Login

News