Can't load rJava on MacOS Mojave and R 3.5.2

Question

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

score 1 · Answer 1 · answered Mar 08 '19 at 19:10

1

I had a similar problem. Its usually best if you start from scratch if you have tried all these solutions and nothing worked. You wouldnt want one of these "fixes" to cause you more issues because most of them require you to change environment variables.

Here is how I fixed it.

Install the latest JAVA JDK https://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html
Run sudo R CMD javareconf in the terminal. Dont change any of the environment variables on your own.

Hope it helps.

answered Mar 08 '19 at 19:10

Sada93

2,785
1
10
21

Unfortunately didn't work. I've started from scratch, as well. After everything I done I formatted my HD and reinstalled MacOS. – Lucas De Abreu Maia Mar 08 '19 at 22:15
OK, this only works if one is using R terminal. Any idea of why this doesn't work on R GUI? – Lucas De Abreu Maia Mar 10 '19 at 03:02

Oo.oO · Accepted Answer · 2019-03-09T13:33:58.540

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 found

Let'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()

Unfortunately, this is not exactly the same env. Take a look at the update. — Oo.oO, Mar 09 '19 at 07:45
You are right, of course. I was running JDK 11.0.2. sudo R CMD javareconf only works on R terminal, though. Any idea of why this doesn't work on R GUI? Anyway, I just installed JDK 11.0.1 and got it working on R GUI. Thanks a lot! — Lucas De Abreu Maia, Mar 10 '19 at 03:05

Can't load rJava on MacOS Mojave and R 3.5.2

Problem

Attempted Solutions

2 Answers2

Linked