rmacosrjava
Can't load rJava on MacOS Mojave and R 3.5.2
I have asked a similar question before, but didn't get any answers that I could actually implement. I've also read the answers here and here, but couldn't implement any of them (partially because no answer actually retraces all of its steps.
Problem
I'm getting an error when trying to load rJava on R 3.5.2 and MacOS Mojave 10.14.3:
> 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/3.5/Resources/library/rJava/libs/rJava.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/rJava/libs/rJava.so
Reason: image not found
Attempted Solutions
I first tried this solution, which didn't work. Then, based on this answer, I tried the following:
Entered the following on Terminal:
$ /usr/libexec/java_home
/Library/Java/JavaVirtualMachines/jdk-11.0.2.jdk/Contents/Home
Then tried the following on R:
> options("java.home"="/Library/Java/JavaVirtualMachines/jdk-11.0.2.jdk/Contents/Home")
>
> Sys.setenv(LD_LIBRARY_PATH='$JAVA_HOME/server')
>
> dyn.load('/Library/Java/JavaVirtualMachines/jdk-11.0.2.jdk/Contents/Home/lib/server/libjvm.dylib')
>
> library(rJava)
Error: package or namespace load failed for ‘rJava’:
.onLoad failed in loadNamespace() for 'rJava', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so, 6): Library not loaded: /Library/Java/JavaVirtualMachines/jdk-11.0.1.jdk/Contents/Home/lib/server/libjvm.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so
Reason: image not found
I've also tried:
> options("java.home"="/Library/Java/JavaVirtualMachines/jdk-11.0.2.jdk/Contents/Home/bin")
> Sys.setenv(LD_LIBRARY_PATH='$JAVA_HOME/server')
> dyn.load('/Library/Java/JavaVirtualMachines/jdk-11.0.2.jdk/Contents/Home/lib/server/libjvm.dylib')
> 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/3.5/Resources/library/rJava/libs/rJava.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/rJava/libs/rJava.so
Reason: image not found
In the past, I've downgraded succesfully to R 3.1, but I'd rather not have to do that every time I want to use rJava
Solution
This is the setup that works for me
macOS Mojave - 10.14.3
XQuartz - version 2.7.11 - https://www.xquartz.org
R - version 5.3.2
> R --version R version 3.5.2 (2018-12-20) -- "Eggshell Igloo" Copyright (C) 2018 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 the terms of the GNU General Public License versions 2 or 3. For more information about these matters see http://www.gnu.org/licenses/.Java - 11.0.1
> java -version java version "11.0.1" 2018-10-16 LTS Java(TM) SE Runtime Environment 18.9 (build 11.0.1+13-LTS) Java HotSpot(TM) 64-Bit Server VM 18.9 (build 11.0.1+13-LTS, mixed mode)rJava - installed from CRAN
> > install.packages("rJava") --- Please select a CRAN mirror for use in this session --- Fontconfig warning: ignoring UTF-8: not a valid region tag trying URL 'https://cloud.r-project.org/bin/macosx/el- capitan/contrib/3.5/rJava_0.9-10.tgz' Content type 'application/x-gzip' length 739259 bytes (721 KB) ================================================== downloaded 721 KB The downloaded binary packages are in /var/folders/... > library(rJava) >
Update
In your case, it looks like JDK used during installation/compilation of rJava is missing. You can tell that from the message:
dlopen(/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/rJava/libs/rJava.so
Reason: image not found
Make sure this file exists:
/Library/Java/JavaVirtualMachines/jdk-11.0.1.jdk/Contents/Home/lib/server/libjvm.dylib
Probably, it's missing. You have two options here: install Java 11.0.1, reconfigure R.
You can list all the available JVM installations using /usr/libexec/java_home -V
Reproducing initial issue, and fixing it
Let's pretend we have removed JDK 11.0.1
> pwd /Library/Java/JavaVirtualMachines > tree -L 1 . |-- jdk-11.0.1.jdk~ `-- jdk-11.0.2.jdk > java -version java version "11.0.2" 2019-01-15 LTS Java(TM) SE Runtime Environment 18.9 (build 11.0.2+9-LTS) Java HotSpot(TM) 64-Bit Server VM 18.9 (build 11.0.2+9-LTS, mixed mode)Let's try to load rJava
> R R version 3.5.2 (2018-12-20) -- "Eggshell Igloo" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin15.6.0 (64-bit) ... ... ... > 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/3.5/Resources/library/rJava/libs/rJava.so': dlopen(/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/rJava/libs/rJava.so Reason: image not foundLet's fix it
> sudo R CMD javareconf Java interpreter : /usr/bin/java Java version : 11.0.2 Java home path : /Library/Java/JavaVirtualMachines/jdk-11.0.2.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-11.0.2.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk-11.0.2.jdk/Contents/Home/include/darwin -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-11.0.2.jdk/Contents/Home/lib/server -ljvm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation JAVA_HOME : /Library/Java/JavaVirtualMachines/jdk-11.0.2.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.It should work now
> R R version 3.5.2 (2018-12-20) -- "Eggshell Igloo" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin15.6.0 (64-bit) ... ... ... > library(rJava) > quit()
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