Ok, flag me for the annoying category of people who start to answer their own questions (though still no solution).
I just noticed that while JAVA_HOME is pointing to the Sun version of Java, the variables javareconf fills in are for openjdk, the open source version of Java that I believe is auto-installed with Ubuntu. (Does anyone know for sure?) I also noticed that while the jre for openjdk is installed in my system, the jdk, which presumably has the compiler info, is not installed. I installed it, ran javareconf again and, eureka!, my cpp flags according to javareconf seem to be good. I see: ## cpp flags : '-I/usr/lib/jvm/java-6-openjdk/jre/../include' ## Triumphantly, I rerun the package update in R, but now get this error (and something nearly identical for JGR itself): ## checking JNI data types... configure: error: One or more JNI types differ from the corresponding native type. You may need to use non-standard compiler flags or a different compiler in order to fix this. ERROR: configuration failed for package ‘rJava’ ## I'm guessing that rJava was compiled w/ Sun's Java and is balking at openjdk. From where I sit, it looks like there's a possible problem with javareconf because it doesn't take JAVA_HOME, which points to Sun's Java. So, I'm guessing I need to get javareconf to use Sun's Java. I used this to reset my default Java: ## sudo update-alternatives --config java ## On resetting to Sun's Java, it still shows openjdk as 'auto', but the Sun Java gets starred. I run javareconf, which now points the Java home path to: /usr/lib/jvm/java-6-sun-1.6.0.20/jre. However, it continues to tell me that JAVA_HOME is not a valid path even though JAVA_HOME continues to reference Sun's jvm directory. (cpp flags also now correctly point to Sun's Java, according to the compiler.) When I run package update, compiling seems to work for JavaGD at least, but after the compile I get: ## ** testing if installed package can be loaded Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared library '/usr/local/lib/R/site-library/JavaGD/libs/JavaGD.so': libjvm.so: cannot open shared object file: No such file or directory ERROR: loading failed * removing ‘/usr/local/lib/R/site-library/JavaGD’ * restoring previous ‘/usr/local/lib/R/site-library/JavaGD’ ## JavaGD.so appears to be in the proper directory, but I'm looking at the restored version. And, yes, I'm running everything as root. In the same run, when it gets to rJava, I have the same error as for rJava running with openjdk: JNI types differ from the native type. So, now I'm really stumped. Again, perhaps this needs to be mentioned to the tech people who put javareconf or perhaps Ubuntu's handling of Java together, but I'm not sure where to do so. _______________________________________________ R-SIG-Debian mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-debian
