I'm trying to config R with Java and after I run sudo R CMD javareconf
I get this.
sudo R CMD javareconf 12:16:29 23.11.17
Java interpreter : /usr/bin/java
Java version : 9.0.1
Java home path : /Library/Java/JavaVirtualMachines/jdk-9.0.1.jdk/Contents/Home
Java compiler : /usr/bin/javac
Java headers gen.: /usr/bin/javah
Java archive tool: /usr/bin/jar
System Java on macOS
trying to compile and link a JNI program
detected JNI cpp flags : -I/System/Library/Frameworks/JavaVM.framework/Headers
detected JNI linker flags : -framework JavaVM
clang -I/usr/local/Cellar/r/3.4.2/lib/R/include -DNDEBUG -I/System/Library/Frameworks/JavaVM.framework/Headers -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/include -fPIC -g -O2 -c conftest.c -o conftest.o
conftest.c:1:10: fatal error: 'jni.h' file not found
#include <jni.h>
^~~~~~~
1 error generated.
make: *** [conftest.o] Error 1
Unable to compile a JNI program
JAVA_HOME : /Library/Java/JavaVirtualMachines/jdk-9.0.1.jdk/Contents/Home
Java library path:
JNI cpp flags :
JNI linker flags :
Updating Java configuration in /usr/local/Cellar/r/3.4.2/lib/R
Done.
I'm concerned by the fatal error: 'jni.h' file not found
.
As a result I can install rJava.
Any idea? thanks!
OK !
seems that I fixed the issue reinstalling R with java
brew reinstall R --with-openblas --with-java
and then I run sudo R CMD javareconf \\ JAVA_CPPFLAGS='-I/System/Library/Frameworks/JavaVM.framework/Headers -I/Library/Java/JavaVirtualMachines/jdk-9.0.1.jdk/
with the following output:
/usr/local/Cellar/r/3.4.2/lib/R/bin/javareconf: line 66: -I/Library/Java/JavaVirtualMachines/jdk-9.0.1.jdk/: No such file or directory
Java interpreter : /Library/Java/JavaVirtualMachines/jdk-9.0.1.jdk/Contents/Home/bin/java
Java version : 9.0.1
Java home path : /Library/Java/JavaVirtualMachines/jdk-9.0.1.jdk/Contents/Home
Java compiler : /Library/Java/JavaVirtualMachines/jdk-9.0.1.jdk/Contents/Home/bin/javac
Java headers gen.: /Library/Java/JavaVirtualMachines/jdk-9.0.1.jdk/Contents/Home/bin/javah
Java archive tool: /Library/Java/JavaVirtualMachines/jdk-9.0.1.jdk/Contents/Home/bin/jar
System Java on macOS
trying to compile and link a JNI program
detected JNI cpp flags : -I/System/Library/Frameworks/JavaVM.framework/Headers
detected JNI linker flags : -framework JavaVM
clang -I/usr/local/Cellar/r/3.4.2/lib/R/include -DNDEBUG -I/System/Library/Frameworks/JavaVM.framework/Headers -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/include -fPIC -I/Library/Java/JavaVirtualMachines/jdk-9.0.1.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk-9.0.1.jdk/Contents/Home/include/darwin -c conftest.c -o conftest.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/Cellar/r/3.4.2/lib/R/lib -L/usr/local/opt/openblas/lib -L/usr/local/opt/gettext/lib -L/usr/local/opt/readline/lib -L/usr/local/lib -o conftest.so conftest.o -framework JavaVM -L/usr/local/Cellar/r/3.4.2/lib/R/lib -lR -lintl -Wl,-framework -Wl,CoreFoundation
JAVA_HOME : /Library/Java/JavaVirtualMachines/jdk-9.0.1.jdk/Contents/Home
Java library path:
JNI cpp flags : -I/System/Library/Frameworks/JavaVM.framework/Headers
JNI linker flags : -framework JavaVM
Updating Java configuration in /usr/local/Cellar/r/3.4.2/lib/R
Done.
I set JAVA_HOME as:
export JAVA_HOME="$(/usr/libexec/java_home)"
Is this correct? or is it better not define JAVA_HOME?
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