[R-SIG-Mac] Problems loading Java libraries in R 2.2.1 OS X 10.4.5, Java 1.5.0 rev 3

[Simon Urbanek]

Marc,

I have no idea about RMAGEML, but in general the Java version is  
determined by the compiler flags used. If the configure script is  
reasonable, it should be using -framework JavaVM to link to JNI in  
which case the used version is determined solely by the
/System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK
softlink.
Quick check shows that RMAGEML is one of the few BioC packages that  
fails to build on OS X, because its configure script is nether  
checking nor detecting Java. I'd recommend you to talk to the  
maintainer. Java detection is now part of several packages (e.g.  
rJava on CRAN) and also R itself, so it should not be hard to fix it.  
Of course, chances are that compiler flags are just one part of the  
problem, and the segfault is caused by something else, but better  
start fixing things from the bottom ;).

Cheers,
Simon


On Apr 5, 2006, at 12:02 PM, Marc Saric wrote:

> Hi list,
>
> I have a PowerMac G5 running OS X 10.4.5 and Java 1.5.0 rev_3 together
> with the precompiled R Version 2.2.1  (2005-12-20 r36812) from CRAN.
>
> I tried to install a Bioconductor package called RMAGEML which depends
> on an external Java-tool for data parsing and loading.
>
> Compilation went fine after some configuration issues but the program
> crashes with a "Bus error" while parsing testdata with the Java- 
> module,
> see below.
> [...]