Simon Urbanek wrote: > 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.
That's exactly what I thought after my initial try to compile the package did not work (except that it was not clear to me wether the "CurrentJDK" link was the only place where things could go wrong). So I did check my setup: lrwxr-xr-x 1 root wheel 3 Nov 8 10:47 CurrentJDK -> 1.5 which in turn points to 1.5.0, so this should be correct. > 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 ;). You are right here, the package does not check for the correct Java automatically, but has to be forced to do it correctly. I managed to compile it by unpacking the tar.gz and hand-editing RMAGEML/src/Makevars (and Makevars.perm and Makevars.in) so that it looks like this # for macosx of 3/05 # PKG_CPPFLAGS=-I/System/Library/Frameworks/JavaVM.framework/Headers PKG_LIBS=-framework JavaVM after that it compiled (actually this code was in the Makevars script allready and just had to be uncommented -a more clever Makevars should fix this). At least the PKG_CPPFLAGS points to lrwxr-xr-x 1 root wheel 24 Apr 5 14:56 Headers -> Versions/Current/Headers which should be ok (see above). Will have a closer look at the CPPFLAGS and LIBS settings and try to find out some more stuff about Java on Mac and try again. P.S. Got mail from the original author, he mentions that no one tried to compile it on Mac so far -might become interresting. :-) -- Bye, Marc Saric _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
