Hi! I’m on macOS 10.13.3 and just installed the new Java 10 using Homebrew Cask. I also have installed R with Homebrew. Everything seems to work fine, however I just get different outputs if I run sudo R CMD javareconf or R CMD javareconf. With sudo I get pointed to Java 9 and without sudo I get pointed to Java 10. I really don’t know why.
Without sudo: $ R CMD javareconf Java interpreter : /Library/Java/JavaVirtualMachines/jdk-10.jdk/Contents/Home/bin/java Java version : 10 Java home path : /Library/Java/JavaVirtualMachines/jdk-10.jdk/Contents/Home Java compiler : /Library/Java/JavaVirtualMachines/jdk-10.jdk/Contents/Home/bin/javac Java headers gen.: /usr/bin/javah Java archive tool: /Library/Java/JavaVirtualMachines/jdk-10.jdk/Contents/Home/bin/jar Non-system Java on macOS trying to compile and link a JNI program detected JNI cpp flags : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/darwin detected JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm /usr/local/opt/llvm/bin/clang -I/usr/local/Cellar/r/3.4.4/lib/R/include -DNDEBUG -I/Library/Java/JavaVirtualMachines/jdk-10.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk-10.jdk/Contents/Home/include/darwin -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c conftest.c -o conftest.o /usr/local/opt/llvm/bin/clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/opt/gettext/lib -L/usr/local/opt/llvm/lib -Wl,-rpath,/usr/local/opt/llvm/lib -L/usr/local/Cellar/r/3.4.4/lib/R/lib -L/usr/local/opt/gettext/lib -L/usr/local/opt/llvm/lib -Wl,-rpath,/usr/local/opt/llvm/lib -o conftest.so conftest.o -L/Library/Java/JavaVirtualMachines/jdk-10.jdk/Contents/Home/lib/server -ljvm -L/usr/local/Cellar/r/3.4.4/lib/R/lib -lR -lintl -Wl,-framework -Wl,CoreFoundation JAVA_HOME : /Library/Java/JavaVirtualMachines/jdk-10.jdk/Contents/Home 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 /usr/local/Cellar/r/3.4.4/lib/R override rw-r--r-- root/admin for /usr/local/Cellar/r/3.4.4/lib/R/etc/Makeconf? (y/n [n]) y override rw-r--r-- root/admin for /usr/local/Cellar/r/3.4.4/lib/R/etc/ldpaths? (y/n [n]) y Done. With sudo: $ sudo R CMD javareconf Java interpreter : /Library/Java/JavaVirtualMachines/jdk-9.0.4.jdk/Contents/Home/bin/java Java version : 9.0.4 Java home path : /Library/Java/JavaVirtualMachines/jdk-9.0.4.jdk/Contents/Home Java compiler : /Library/Java/JavaVirtualMachines/jdk-9.0.4.jdk/Contents/Home/bin/javac Java headers gen.: /Library/Java/JavaVirtualMachines/jdk-9.0.4.jdk/Contents/Home/bin/javah Java archive tool: /Library/Java/JavaVirtualMachines/jdk-9.0.4.jdk/Contents/Home/bin/jar Non-system Java on macOS trying to compile and link a JNI program detected JNI cpp flags : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/darwin detected JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm /usr/local/opt/llvm/bin/clang -I/usr/local/Cellar/r/3.4.4/lib/R/include -DNDEBUG -I/Library/Java/JavaVirtualMachines/jdk-9.0.4.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk-9.0.4.jdk/Contents/Home/include/darwin -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c conftest.c -o conftest.o /usr/local/opt/llvm/bin/clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/opt/gettext/lib -L/usr/local/opt/llvm/lib -Wl,-rpath,/usr/local/opt/llvm/lib -L/usr/local/Cellar/r/3.4.4/lib/R/lib -L/usr/local/opt/gettext/lib -L/usr/local/opt/llvm/lib -Wl,-rpath,/usr/local/opt/llvm/lib -o conftest.so conftest.o -L/Library/Java/JavaVirtualMachines/jdk-9.0.4.jdk/Contents/Home/lib/server -ljvm -L/usr/local/Cellar/r/3.4.4/lib/R/lib -lR -lintl -Wl,-framework -Wl,CoreFoundation JAVA_HOME : /Library/Java/JavaVirtualMachines/jdk-9.0.4.jdk/Contents/Home 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 /usr/local/Cellar/r/3.4.4/lib/R Done. The result of be pointed to Java 10 is rJava package not be able to build. warning: [options] bootstrap class path not set in conjunction with -source 6 warning: [options] source value 6 is obsolete and will be removed in a future release warning: [options] target value 1.6 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 4 warnings /usr/bin/javah -d . -classpath . org.rosuda.JRI.Rengine Unable to locate an executable at "/Library/Java/JavaVirtualMachines/jdk-10.jdk/Contents/Home/bin/javah" (-1) make[2]: *** [org_rosuda_JRI_Rengine.h] Error 2 make[1]: *** [src/JRI.jar] Error 2 make: *** [jri] Error 2 ERROR: compilation failed for package ‘rJava’ * removing ‘/Users/lpuerto/Library/R/3.x/library/rJava’ * restoring previous ‘/Users/lpuerto/Library/R/3.x/library/rJava’ The downloaded source packages are in ‘/private/var/folders/wf/41gjf2mx7m7fmvfd8dr22_5h0000gn/T/RtmpT2kJMY/downloaded_packages’ Warning message: In install.packages("rJava", repos = "cloud.r-project.org") : installation of package ‘rJava’ had non-zero exit status I've checked and there isn't a javah on /Library/Java/JavaVirtualMachines/jdk-10.jdk/Contents/Home/bin/javah as in Java 9. Which make me think that either R CMD javareconf isn’t working properly with Java 10 or rJava is not yet compatible with Java 10. Does anyone know what is going on? Thanks! PS/ I’ve opened an issue <https://github.com/s-u/rJava/issues/137> in rJava’s github and a question in stackoverflow <https://stackoverflow.com/questions/49519007/sudo-r-cmd-javareconf-and-r-cmd-javareconf-produce-different-output-with-java-10>. Best Regards Luis Puerto http://luisspuerto.net [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.