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rjava

compile rJava with jdk1.8.0_05


I am trying to compile rJava using on OSX 10.7.5

install.packages("rJava",type="source")

The motive is this. I am using code compiled with jdk1.8.0_05 and call it using rJava. When I do this there is a mismatch between the class file version of code compiled with jdk1.8.0_05 and the class files rJava recognizes.

 llvm-gcc-4.2 -arch x86_64 -std=gnu99 -c -o rjava.o rjava.c -g -Iinclude  -DRIF_HAS_CSTACK    
-DRIF_HAS_RSIGHAND -mtune=core2 -g -O2  - 
I/Library/Java/JavaVirtualMachines/jdk1.8.0_05.jdk/Contents/Home/jre/../include -
I/Library/Java/JavaVirtualMachines/jdk1.8.0_05.jdk/Contents/Home/jre/../include/darwin  -
fno-common -
I/Library/Java/JavaVirtualMachines/jdk1.8.0_05.jdk/Contents/Home/jre/../include -
I/Library/Java/JavaVirtualMachines/jdk1.8.0_05.jdk/Contents/Home/jre/../include/darwin
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -o libjri.jnilib Rengine.o jri.o Rcallbacks.o Rinit.o  
globals.o rjava.o  -dynamiclib -framework JavaVM -F/Library/Frameworks/R.framework/.. - 
framework R -llzma -licucore -lm -liconv
ld: library not found for -llzma
collect2: ld returned 1 exit status
make[2]: *** [libjri.jnilib] Error 1
make[1]: *** [src/JRI.jar] Error 2
make: *** [jri] Error 2
ERROR: compilation failed for package ‘rJava’

I have installed xz using homebrew but that didn't help.

Can I not use rJava to call code compiled with jdk1.8.0_05 ?

rJava binaries are installed and working properly. It is the source compilation that causes this.

I have executed R CMD javareconf.

Java interpreter : /usr/bin/java
Java version     : 1.8.0_05
Java home path   : /Library/Java/JavaVirtualMachines/jdk1.8.0_05.jdk/Contents/Home/jre
Java compiler    : /usr/bin/javac
Java headers gen.: /usr/bin/javah
Java archive tool: /usr/bin/jar
Non-system Java on OS X

trying to compile and link a JNI progam 
detected JNI cpp flags    : -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/darwin
detected JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -   
DNDEBUG -I/Library/Java/JavaVirtualMachines/jdk1.8.0_05.jdk/Contents/Home/jre/../include - 
 I/Library/Java/JavaVirtualMachines/jdk1.8.0_05.jdk/Contents/Home/jre/../include/darwin -  
I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c conftest.c -o conftest.o

llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o conftest.so conftest.o -L/Library/Java/JavaVirtualMachines/jdk1.8.0_05.jdk/Contents/Home/jre/lib/server -ljvm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation


JAVA_HOME        : /Library/Java/JavaVirtualMachines/jdk1.8.0_05.jdk/Contents/Home/jre
Java library path: $(JAVA_HOME)/lib/server
JNI cpp flags    : -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/darwin

JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm
Updating Java configuration in /Library/Frameworks/R.framework/Resources
Done.

Solution

  • You need a library: "library not found for -llzma"

    Try download and install XZ 5.0.7: http://macpkg.sourceforge.net/