Hi folks: I'm trying to update my JGR and related packages, but run into a compile problem, that I suspect must be affecting others. I get this output when compiling rJava, JavaGD, etc.:
## checking Java support in R... present: interpreter : '/usr/bin/java' cpp flags : '' java libs : '-L/usr/lib/jvm/java-6-openjdk/jre/lib/amd64/server -L/usr/lib/jvm/java-6-openjdk/jre/lib/amd64 -L/usr/lib/jvm/java-6-openjdk/jre/../lib/amd64 -L -L/usr/java/packages/lib/amd64 -L/usr/lib/jni -L/lib -L/usr/lib -ljvm' configure: error: One or more Java configuration variables are not set. Make sure R is configured with full Java support (including JDK). Run R CMD javareconf as root to add Java support to R. ## When I run R CMD javareconf as root, I get: ## # R CMD javareconf *** JAVA_HOME is not a valid path, ignoring Java interpreter : /usr/bin/java Java version : 1.6.0_0 Java home path : /usr/lib/jvm/java-6-openjdk/jre Java compiler : /usr/bin/javac Java headers gen.: /usr/bin/javah Java archive tool: /usr/bin/jar Java library path: $(JAVA_HOME)/lib/amd64/server:$(JAVA_HOME)/lib/amd64:$(JAVA_HOME)/../lib/amd64::/usr/java/packages/lib/amd64:/usr/lib/jni:/lib:/usr/lib JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -L$(JAVA_HOME)/lib/amd64 -L$(JAVA_HOME)/../lib/amd64 -L -L/usr/java/packages/lib/amd64 -L/usr/lib/jni -L/lib -L/usr/lib -ljvm JNI cpp flags : Updating Java configuration in /etc/R Done. ## When I investigate JAVA_HOME, I get: ## # echo $JAVA_HOME /usr/lib/jvm/java-6-sun # ls /usr/lib/jvm/java-6-sun bin docs include lib man THIRDPARTYLICENSEREADME.txt COPYRIGHT ext jre LICENSE README.html ## So, JAVA_HOME does point to a proper installation of Sun's Java, so far as I can tell. The cpp flag seems to be the big problem, but I don't know enough about this setup to figure out how to fix it. I get R from the software source: http://lib.stat.cmu.edu/R/CRAN/bin/linux/ubuntu. Just installed R version 2.11.1 (2010-05-31) My operating system is 9.10 Karmic, kernel 2.6.31-22-generic. I'm guessing that either there's a bug in javareconf or in the Sun Java installation on my version of Ubuntu. Not sure if there's a workaround or whether there is some bug bboard to which I should report this. Suggestions welcome! _______________________________________________ R-SIG-Debian mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-debian
