[R-SIG-Mac] Problems running rJava in MacOS

[David Winsemius]

Was there a reason to refuse the system's offer to override?


-- 

David.

On 9/4/19 4:30 PM, Manuel Spínola wrote:
> Dear list members,
>
> I am having troubles running rJava.
>
> MacOS 10.14.6
> R 3.6.1
> rJava 0.9-11
> jdk 11.0.4
>
>> library(rJava)
> Error: package or namespace load failed for ‘rJava’:
>   .onLoad failed in loadNamespace() for 'rJava', details:
>    call: dyn.load(file, DLLpath = DLLpath, ...)
>    error: unable to load shared object
> '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so':
>
> dlopen(/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so,
> 6): Library not loaded:
> /Library/Java/JavaVirtualMachines/jdk-11.0.1.jdk/Contents/Home/lib/server/libjvm.dylib
>    Referenced from:
> /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so
>    Reason: image not found
>
> I run in terminal
>
> (base) Manuels-MacBook-Pro:~ manuelspinola$ R CMD javareconf
>
> Java interpreter : /usr/bin/java
>
> Java version     : 11.0.4
>
> Java home path   :
> /Library/Java/JavaVirtualMachines/jdk-11.0.4.jdk/Contents/Home
>
> Java compiler    : /usr/bin/javac
>
> Java headers gen.: /usr/bin/javah
>
> Java archive tool: /usr/bin/jar
>
>
> 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
>
> clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
> -I/Library/Java/JavaVirtualMachines/jdk-11.0.4.jdk/Contents/Home/include
> -I/Library/Java/JavaVirtualMachines/jdk-11.0.4.jdk/Contents/Home/include/darwin
> -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
> -I/usr/local/include  -fPIC  -Wall -g -O2  -c conftest.c -o conftest.o
>
> clang -dynamiclib -Wl,-headerpad_max_install_names -undefined
> dynamic_lookup -single_module -multiply_defined suppress
> -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o
> conftest.so conftest.o
> -L/Library/Java/JavaVirtualMachines/jdk-11.0.4.jdk/Contents/Home/lib/server
> -ljvm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
> -Wl,CoreFoundation
>
>
>
> JAVA_HOME        :
> /Library/Java/JavaVirtualMachines/jdk-11.0.4.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 /Library/Frameworks/R.framework/Resources
>
> override rw-r--r--  root/admin for
> /Library/Frameworks/R.framework/Resources/etc/Makeconf? (y/n [n])
>
>