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. 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] -- View this message in context: http://r.789695.n4.nabble.com/JGR-Segmentation-fault-tp4401260p4401260.html Sent from the R help mailing list archive at Nabble.com.
JGR Segmentation fault
4 messages · dberringer, 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] -- View this message in context: http://r.789695.n4.nabble.com/JGR-Segmentation-fault-tp4401260p4401260.html Sent from the R help mailing list archive at Nabble.com.
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1 day later
The http://mxcl.github.com/homebrew/ Homebrew package manager is an exelent way to manage packages like R on osx. I highly recommend it to any developer. I am hoping there are others in the R community that are interested in getting this working too. Does anyone else run a Homebrew install of R? If so have you been able to get JGR / Deducer running? -- View this message in context: http://r.789695.n4.nabble.com/JGR-Segmentation-fault-tp4401260p4404821.html Sent from the R help mailing list archive at Nabble.com.
3 days later
Ok. So I'm a little closer to figuring this thing out. I didn't realize I needed to run the javareconf command as root like so. sudo R CMD javareconf JAVA_CPPFLAGS=-I/System/Library/Frameworks/JavaVM.framework/Headers I'm not getting the permission issue anymore but I'm still getting the segmentation fault error: => /Users/User/jgrLaunch ; exit; Loading preferences from /Users/User/.JGRprefsrc JGR R_HOME: /usr/local/Cellar/r/2.14.1/R.framework/Resources libroot: /usr/local/Cellar/r/2.14.1/R.framework/Versions/2.14/Resources/library/ Attempting to load jnilib: /usr/local/Cellar/r/2.14.1/R.framework/Versions/2.14/Resources/library/rJava/jri/libjri.jnilib Segmentation fault logout [Process completed] I also got this error from the R console: Feb 23 22:50:59 grizz R[46063] <Error>: kCGErrorInvalidConnection: CGSGetWindowTags: Invalid connection Feb 23 22:50:59 grizz R[46063] <Error>: kCGErrorFailure: Set a breakpoint @ CGErrorBreakpoint() to catch errors as they are logged. Feb 23 23:07:44 grizz R[46063] <Error>: kCGErrorInvalidConnection: CGSGetWindowTags: Invalid connection Any help would be awesome. -- View this message in context: http://r.789695.n4.nabble.com/JGR-Segmentation-fault-tp4401260p4416432.html Sent from the R help mailing list archive at Nabble.com.