Well this is interesting. I have a working java setup (using OpenJDK). But I can break it by running "R CMD javareconf -e". This command exports a number of JAVA_* environment variables. The rJava configure script uses these instead of querying R, but the compilation then fails.
It seems that the crucial difference is that the environment variables JAVA_CPPFLAGS and JAVA_LIBS contain references to JAVA_HOME that are not expanded. With the non-working configuration I get this output from the configure script: cpp flags : '-I$(JAVA_HOME)/../include -I $(JAVA_HOME)/../include/linux' java libs : '-L$(JAVA_HOME)/lib/amd64/server -L$(JAVA_HOME)/lib/amd64 -L$(JAVA_HOME)/../lib/amd64 -L -L/usr/java/packages/lib/amd64 -L/usr/lib64 -L/lib64 -L/lib -L/usr/lib -ljvm' Whereas with the working R configuration I get the fully expanded version: cpp flags : '-I/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/../include -I/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/../include/linux' java libs : '-L/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/lib/amd64/server -L/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/lib/amd64 -L/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/../lib/amd64 -L -L/usr/java/packages/lib/amd64 -L/usr/lib64 -L/lib64 -L/lib -L/usr/lib -ljvm' Try compiling in a new shell without exporting any of these JAVA_* variables. Martyn On Wed, 2008-10-22 at 12:00 +0100, Paulo Cortez wrote: > Thanks for the many answers I received. > > This is becoming a nightmare and I am concluding that installing java1.6 > in CentOS5 is particularly hard, specially if you installed previous jdk > versions... > > I tryed a wide range of solutions. I resume some of them: > > 1) Tryed to reinstall jdk1.6 and use update-alternatives command; > 1) The CentOS5 howto java guide is outdated and does not work > (http://wiki.centos.org/HowTos/JavaOnCentOS); > 2) I installed openjdk, from: http://openjdk.java.net/install/ > I checked if the java was updated with: > $alternatives --config java > > There are 2 programs which provide 'java'. > > Selection Command > ----------------------------------------------- > 1 /usr/lib/jvm/jre-1.4.2-gcj/bin/java > *+ 2 /usr/lib/jvm/jre-1.6.0-openjdk/bin/java > > Then, after several R CMD javareconf attemps I got: > > ------ > Java interpreter : /usr/bin/java > Java version : 1.6.0_0 > Java home path : /usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0/jre > Java compiler : /usr/bin/javac > Java headers gen.: /usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0/jre/../bin/javah > Java archive tool: /usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0/jre/../bin/jar > Java library path: > $(JAVA_HOME)/lib/i386/server:$(JAVA_HOME)/lib/i386:$(JAVA_HOME)/../lib/i386::/usr/java/packages/lib/i386:/lib:/usr/lib > JNI linker flags : -L$(JAVA_HOME)/lib/i386/server > -L$(JAVA_HOME)/lib/i386 -L$(JAVA_HOME)/../lib/i386 -L > -L/usr/java/packages/lib/i386 -L/lib -L/usr/lib -ljvm > JNI cpp flags : -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/linux > > Updating Java configuration in /usr/lib/R > Done. > ------ > The link files are ok: > $ ls -la /usr/bin/ja* > lrwxrwxrwx 1 root root 8 Apr 11 2008 /usr/bin/jade -> openjade > lrwxrwxrwx 1 root root 48 Oct 22 10:52 /usr/bin/java -> > /usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0/bin/java > lrwxrwxrwx 1 root root 49 Oct 22 10:52 /usr/bin/javac -> > /usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0/bin/javac > lrwxrwxrwx 1 root root 51 Oct 22 11:19 /usr/bin/javadoc -> > /usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0/bin/javadoc > lrwxrwxrwx 1 root root 49 Oct 22 11:18 /usr/bin/javah -> > /usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0/bin/javah > lrwxrwxrwx 1 root root 50 Oct 22 10:52 /usr/bin/javaws -> > /usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0/bin/javaws > > But then I try: > $ R CMD INSTALL rJava (the rJava.tar.gz was unpacked) > ... > checking whether JNI programs can be compiled... configure: error: > Cannot compile a simple JNI program. See config.log for details. > --------- > Opening the config.log file I get: > --------- > configure:3880: checking whether JNI programs can be compiled > configure:3898: gcc -o conftest -O3 -g -std=gnu99 > -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/linux conftest.c > -L$(JAVA_HOME)/lib/i386/server -L$(JAVA_HOME)/l > ib/i386 -L$(JAVA_HOME)/../lib/i386 -L -L/usr/java/packages/lib/i386 > -L/lib -L/usr/lib -ljvm >&5 > /usr/bin/ld: cannot find -ljvm > collect2: ld returned 1 exit status > configure:3904: $? = 1 > configure: failed program was: > | > | #include <jni.h> > | int main(void) { > | jobject o; > | JNI_CreateJavaVM(0, 0, 0); > | return 0; > | } > | > configure:3920: error: Cannot compile a simple JNI program. See > config.log for details. > > All these attempts took 2 hours of my life, with no results :((( > > Regards, ----------------------------------------------------------------------- This message and its attachments are strictly confidenti...{{dropped:8}} ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
