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

[Manuel Spínola]

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])


-- 
*Manuel Spínola, Ph.D.*
Instituto Internacional en Conservación y Manejo de Vida Silvestre
Universidad Nacional
Apartado 1350-3000
Heredia
COSTA RICA
mspinola using una.cr <mspinola using una.ac.cr>
mspinola10 using gmail.com
Teléfono: (506) 8706 - 4662
Personal website: Lobito de río <https://sites.google.com/site/lobitoderio/>
Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/>

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