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
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