rJava image missing in Rstudio in OsX - rstudio

Question

When I try to load library("rJava") in RStudio on OsX High Sierra, I get the error already mentioned about the image not being present:
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 '/Users/ognjenmilicevic/RPlay/Methylation_Mayo_Vesna_Garovic/libs/rJava/libs/rJava.so':
dlopen(/Users/ognjenmilicevic/RPlay/Methylation_Mayo_Vesna_Garovic/libs/rJava/libs/rJava.so, 6): Library not loaded: /Library/Java/JavaVirtualMachines/jdk-11.0.1.jdk/Contents/Home/lib/server/libjvm.dylib
Referenced from: /Users/ognjenmilicevic/RPlay/Methylation_Mayo_Vesna_Garovic/libs/rJava/libs/rJava.so
Reason: image not found
I tried reconfiguring Java but the error persists:
$ R CMD javareconf
Java interpreter : /usr/bin/java
Java version : 10.0.1
Java home path : /Library/Java/JavaVirtualMachines/jdk-10.0.1.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-10.0.1.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk-10.0.1.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-10.0.1.jdk/Contents/Home/lib/server -ljvm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
JAVA_HOME : /Library/Java/JavaVirtualMachines/jdk-10.0.1.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
Done.
Removing and reinstalling the package doesn't help. I tried pointing to my version by using:
dyn.load('/Library/Java/JavaVirtualMachines/jdk-10.0.1.jdk/Contents/Home/lib/server/libjvm.dylib')
The error persists. All the while it works in R when ran as a command. Where is the path "/Library/Java/JavaVirtualMachines/jdk-11.0.1.jdk/Contents/Home/lib/server/libjvm.dylib" coming from and how can I change it to point to my installation?

Answer 1

It looks like you have sort of a messy installation or rJava.
You can always check which version of Java was used (while building rJava) by calling:
> otool -L /Library/Frameworks/R.framework/Resources/library/rJava/libs/rJava.so
/Library/Frameworks/R.framework/Resources/library/rJava/libs/rJava.so:
rJava.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Java/JavaVirtualMachines/jdk-11.0.1.jdk/Contents/Home/lib/server/libjvm.dylib (compatibility version 1.0.0, current version 1.0.0)
/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libR.dylib (compatibility version 3.6.0, current version 3.6.0)
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1259.11.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1226.10.1)
in your case you have to call
> otool -L /Users/ognjenmilicevic/RPlay/Methylation_Mayo_Vesna_Garovic/libs/rJava/libs/rJava.so
Make sure you have this Java version installed: jdk-11.0.1.jdk. If you don't have it, and you want to install rJava with your current release of JDK - e.g.: jdk-10.0.1.jdk, follow the steps here: http://www.owsiak.org/r-java-11-and-making-sure-you-can-load-rjava/
Also, remember that in macOS, the default Java is the newest one. It means that RStudio will pick the version with highest number - one that is enabled.
You can disable given version of Java by calling
> cd /Library/Java/JavaVirtualMachines/jdk-11.0.4.jdk/Contents
> mv Info.plist Info.plist~
Above commands will make this Java version "invisible" for macOS.
Once you follow the steps (as described in linked article) you will be able to run Java from both: R and RStudio
> R
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(rJava)
> .jinit()
> J("java.lang.System","getProperty","java.version")
[1] "11.0.3"
>