rJava on MacOS Sierra 10.12.15: unsupported option

Question

I'm trying to install rJava on MacOS Sierra. Have to tried the tips and guides elsewhere for other other version MacOS such as https://github.com/snowflakedb/dplyr-snowflakedb/wiki/Configuring-R-rJava-RJDBC-on-Mac-OS-X and Install xlsx and rJava on Mac

but it does not work out. Much appreciate any help. Thanks.

My Mac version: macOS Sierra, version 10.12.15 My R version: 3.4.0 (2017-04-21) My Rstudio version: Version 0.99.903

Java version:

bash-3.2$ /usr/libexec/java_home -V
bash-3.2$ java -version
java version "1.8.0_131"
Java(TM) SE Runtime Environment (build 1.8.0_131-b11)
Java HotSpot(TM) 64-Bit Server VM (build 25.131-b11, mixed mode)


bash-3.2$ R CMD javareconf
Java interpreter : /usr/bin/java
Java version     : 1.8.0_131
Java home path   : /Library/Java/JavaVirtualMachines/jdk1.8.0_131.jdk/Contents/Home/jre
Java compiler    : /usr/bin/javac
Java headers gen.: /usr/bin/javah
Java archive tool: /usr/bin/jar
Non-system Java on macOS

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/jdk1.8.0_131.jdk/Contents/Home/jre/../include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_131.jdk/Contents/Home/jre/../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/jdk1.8.0_131.jdk/Contents/Home/jre/lib/server -ljvm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation


JAVA_HOME        : /Library/Java/JavaVirtualMachines/jdk1.8.0_131.jdk/Contents/Home/jre
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]) n
not overwritten
override rw-r--r--  root/admin for /Library/Frameworks/R.framework/Resources/etc/ldpaths? (y/n [n]) n
not overwritten
Done.

When I tried to install rJava, I ran

`R --quiet -e 'install.packages("rJava", type="source", repos="http://cran.us.r-project.org")` 

I got the errors:

clang: error: unsupported option '-fopenmp'
make[2]: *** [libjri.jnilib] Error 1
make[1]: *** [src/JRI.jar] Error 2
make: *** [jri] Error 2
ERROR: compilation failed for package ‘rJava’
* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava’

The downloaded source packages are in
    ‘/private/var/folders/w8/ksbj8dh15bz2lkss7h2tpzk80000gn/T/Rtmp6r9HI0/downloaded_packages’
Warning message:
In install.packages("rJava", type = "source", repos = "http://cran.us.r-project.org") :
  installation of package ‘rJava’ had non-zero exit status

I ran:

"curl -#ROL https://www.rforge.net/rJava/snapshot/rJava_0.9-8.tar.gz
R CMD INSTALL rJava_0.9-8.tar.gz"

and got the following error messages:

clang: error: unsupported option '-fopenmp'
make[2]: *** [libjri.jnilib] Error 1
make[1]: *** [src/JRI.jar] Error 2
make: *** [jri] Error 2
ERROR: compilation failed for package ‘rJava’

* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava’

I dont know what to do. Thanks for your help.

Answer 1

This article here solved this fopenmp issue for me on macOS Sierra 10.12.4. I outlined the solution here but also below. The problem is that forenmp option is not supported in macOS gcc so we have to compile a new version of the gcc.

---

Solution to forenmp problem

I have tested this with Homerew's r-app brew cask install r-app and Oracle's JDK. Then I did the following

brew install homebrew/versions/gcc49 --without-multilib #Long ~70min compiling...
sudo chown -R $(whoami):admin /usr/local
brew link --overwrite --force gcc49
brew unlink gcc49 && brew link gcc49
brew install llvm
mkdir ~/.R; touch ~/.R/Makevars

echo "VER=-4.9 
CC=gcc$(VER)
CXX=g++$(VER)
CXX1X=g++$(VER)
CFLAGS=-mtune=native -g -O2 -Wall -pedantic -Wconversion
CXXFLAGS=-mtune=native -g -O2 -Wall -pedantic -Wconversion
FLIBS=-L/usr/local/Cellar/gcc/4.9.3/lib/gcc/4.9" > ~/.R/Makevars

and now

sudo R CMD javareconf 
Rscript -e 'install.packages("rJava", repos="http://rforge.net", type="source")'

and now rJava is working!

Answer 2

Take a look here:

http://www.owsiak.org/?p=3671

You can find quite detailed description of how to deal with rJava in macOS.

Make sure to install JDK that is provided by Oracle before you proceed.

Answer 3

Comments using OSX 10.12.6 with Java 1.8.0_181 and dealing with the above issue and another issue related to compiling rJava.

First:

Install rJava with these commands:

wget https://cran.r-project.org/src/contrib/rJava_0.9-10.tar.gz
tar xvfz rJava_0.9-10.tar.gz
cd rJava
R CMD INSTALL rJava

Why use R CMD INSTALL? This will keep the config.log file that will allow you to debug things; install.packages() does not and help you get might not be very helpful in that case (e.g. https://github.com/s-u/rJava/issues/111).

Second:

Make sure you run the following, if you've updated Java (remember you need the JDK, not JRE).

sudo R CMD javareconf

Error (checking JNI data types):

To fix this error:

checking JNI data types... configure: error: One or more JNI types differ from the corresponding native type. You may need to use non-standard compiler flags or a different compiler in order to fix this.

do this:

sudo ln -f -s $(/usr/libexec/java_home)/jre/lib/server/libjvm.dylib /usr/local/lib
sudo ln -f -s /usr/local/lib/libjvm.dylib /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/

Error (unsupported option '-fopenmp):

To fix this error:

clang: error: unsupported option '-fopenmp

do the following:

Note: The instructions may need to be modified for newer versions of gcc, but make sure you get a version greater than 7 (see notes that follow); the following command can be used to find out the available versions:

brew search gcc

Then install gcc:

brew install gcc@7
sudo chown -R $(whoami):admin /usr/local
brew link --overwrite --force gcc@7
brew unlink gcc@7 && brew link gcc@7
brew install llvm
mkdir -p ~/.R

## Check the versions and folder in FLIBS match what you install
echo "CC=gcc-7
CXX=g++-7
CXX1X=g++-7
CFLAGS=-mtune=native -g -O2 -Wall -pedantic -Wconversion
CXXFLAGS=-mtune=native -g -O2 -Wall -pedantic -Wconversion
FLIBS=-L/usr/local/Cellar/gcc\@7/7.3.0/lib/gcc/7" > ~/.R/Makevars

Notes: You need any version of gcc greater than 7; the without-multilib flag mentioned in the earlier answer may not be available, but it is important. Why the without-multilib flag?: https://thecoatlessprofessor.com/programming/openmp-in-r-on-os-x/ and OpenMP/gcc on macOS : gcc --without-multilib not available

Then install rJava

R CMD INSTALL rJava

Finally, test library (you should see your Java version):

library(rJava)
.jinit()
.jcall("java/lang/System", "S", "getProperty", "java.runtime.version")