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R install of openmx breaks with R update 3.3.2

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rsphadmin's picture
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Joined: 01/05/2017 - 11:50
R install of openmx breaks with R update 3.3.2
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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:

jpritikin's picture
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Joined: 05/24/2012 - 00:35
gcc

We recommend gcc 5.4. Which version of gcc are you using?

rsphadmin's picture
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Joined: 01/05/2017 - 11:50
gcc 5.4 is not an option

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.

jpritikin's picture
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Joined: 05/24/2012 - 00:35
gcc

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.

rsphadmin's picture
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Joined: 01/05/2017 - 11:50
I have openmx 3.7 installed

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.

jpritikin's picture
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Joined: 05/24/2012 - 00:35
how to build

./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

AdminRobK's picture
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Joined: 01/24/2014 - 12:15
structural-equation modeling or materials science?

Is it possible you want the forum for the "other" OpenM[Xx], http://www.openmx-square.org/forum/patio.cgi ?

rsphadmin's picture
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Joined: 01/05/2017 - 11:50
possible update in instructions

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

jpritikin's picture
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Joined: 05/24/2012 - 00:35
clone

You'll need to clone using the https protocol.

rsphadmin's picture
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Joined: 01/05/2017 - 11:50
got it working sort of

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?

jpritikin's picture
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Joined: 05/24/2012 - 00:35
modules

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.

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