How to Load Rjava on R

Unable to load rJava on R

Use:

Sys.setenv(JAVA_HOME='...path to JRE...')

e.g.

Sys.setenv(JAVA_HOME='C:\\Program Files\\Java\\jdk1.7.0_51\\jre')

Your environment variable is wrong.

Can't load rJava on MacOS Mojave and R 3.5.2

This is the setup that works for me

1. macOS Mojave - 10.14.3

2. XQuartz - version 2.7.11 - https://www.xquartz.org

2. 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/.
   

3. 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)
   

4. 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

1. 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)
   

2. 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
   

3. 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.
   

4. 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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