I've seen a lot of problems on ubuntu systems when users have JAVA_HOME defined in the environment.
Make sure you have a clean env, and try the javareconf. -Whit On Tue, Jun 8, 2010 at 3:22 PM, Dirk Eddelbuettel <[email protected]> wrote: > > Peter, > > On 8 June 2010 at 13:51, Peter Muhlberger wrote: > | Hi folks: I guess my earlier posting was too involved, so let me try > | to get to the essence of my problem. > | > | I recently tried to compile JGR, rJava, etc. into my updated R. > | First, I ran: R CMD javareconf. The output from that tells me that > | "JAVA_HOME is not a valid path, ignoring" and the cpp flags are set to > | nothing. The javareconf fills most of the variables with references > | to openjdk. JAVA_HOME, as far as I can tell, points to a properly > | installed copy of Sun Java. When I run update.packages(checkBuilt=T) > | with this, it unsurprisingly tells me that "One or more Java > | configuration variables are not set" and all of my Java based programs > | fail to compile. > | > | I've tried switching the default Java to the Sun version using "sudo > | update-alternatives --config java". Now, javareconf fills in the cpp > | flag and variables point to the Sun version, though I still get the > | error msg that JAVA_HOME is not a valid path (though javareconf sets > | the home path to: /usr/lib/jvm/java-6-sun-1.6.0.20/jre). When I try > | to compile rJava, I get the error: rJava, "JNI types differ from the > | native type." > | > | Does anyone have any thoughts on how to fix this? Alternatively, is > | there somewhere I can report these problems so they might get fixed in > | future versions? I suspect I can't be the only person having these > | problems. > > Quick caveat: I am not a Java user or programmer. > > That said, I had wanted to get this work for years because several > interesting packages build on-top of rjava. And as of a few years ago it > started to work so I since then I am > > a) instrumenting Debian's r-base-core package to be Java-aware > > b) packaging /maintaining rjava for Debian as well > > but all of that only with the non-Sun packages. E.g. rjava has a > build-depends on openjdk-6-jdk, and that seems to work. So start by > installing that. > > I have also built JGR and other packages, and have the cran2deb robot build > quite a few more. But never with the Sun java, and certainly never when > mixing. > > Beyond that, maybe the Java lists can be of more help than we can here. > > -- > Regards, Dirk > > _______________________________________________ > R-SIG-Debian mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/r-sig-debian > _______________________________________________ R-SIG-Debian mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-debian
