[R] JGR Segmentation fault

[Simon Urbanek]

On Feb 19, 2012, at 2:48 AM, dberringer wrote:

> I have been trying to get JGR up and running but so far no luck.  I installed
> R from source using the homebrew package manager and everything works fine
> and I was able to install JGR and all its dependencies.  Every time I try to
> start JGR I get the error below.  Any idea why I'm getting the Segmentation
> fault?  Thanks.
> 

There are a few fishy things in your output (apart form using homebrew R which has its issues):
a) you get permission denied in the library of your installed R 
b) you are using CRAN R's library path in your home - so potentially you may have a clash of CRAN packages vs homebrew
I would strongly recommend using CRAN R to make your life easier. We don't officially support homebrew R (it is a home brew after all ;)) so you may need to change the launcher if it doesn't follow the same layout as CRAN R. Also it could be an issue in homebrew R - we have seen random segfaults in it before. Finally, if you use Apple's gcc-4.2 and don't disable OpenMP in R it will segfault in any threaded code, including JGR, due to bugs in the old gomp that come with gcc-4.2 (but that comes usually much later when you actually use R).

Cheers,
Simon


> System Info:
> OSX 10.7.2
> R version 2.14.1 (2011-12-22)
> java version "1.6.0_29"
> Java(TM) SE Runtime Environment (build 1.6.0_29-b11-402-11M3527)
> Java HotSpot(TM) 64-Bit Server VM (build 20.4-b02-402, mixed mode)
> 
> Error:
> => /usr/local/Cellar/r/2.14.1/R.framework/Versions/2.14/Resources/jgrLaunch
> ; exit;
> /usr/local/Cellar/r/2.14.1/R.framework/Versions/2.14/Resources/library:
> Permission denied.
> Loading preferences from /Users/User/.JGRprefsrc
> JGR R_HOME: /usr/local/Cellar/r/2.14.1/R.framework/Resources
> libroot: /Users/User/Library/R/2.14/library/
> Attempting to load jnilib:
> /Users/User/Library/R/2.14/library/rJava/jri/libjri.jnilib
> Segmentation fault
> logout
> 
> [Process completed]
> 
> 
> 
> 
> --
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