Hi. Thanks for posting some ideas, I’ve trying to install that for quite some time

I just tried your solution and didn’t work though

If I do
sudo `/usr/libexec/java_home`/../Info.plist
I get
sudo: /Library/Java/JavaVirtualMachines/jdk1.8.0_131.jdk/Contents/Home/../Info.plist: command not found

If I anyways try install.packages(“rJava”, type=”source”)
I get
…
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’
…

Inside my config.log I get
….
configure:2890: checking for ccache /usr/local/opt/gcc/bin/gcc-7 option to accept ISO C89
configure:2953: ccache /usr/local/opt/gcc/bin/gcc-7 -c -Wall -g -O2 conftest.c >&5
configure:2953: $? = 0
configure:2966: result: none needed
configure:2996: checking how to run the C preprocessor
configure:3027: ccache /usr/local/opt/gcc/bin/gcc-7 -E conftest.c
configure:3027: $? = 0
configure:3041: ccache /usr/local/opt/gcc/bin/gcc-7 -E conftest.c
conftest.c:9:10: fatal error: ac_nonexistent.h: No such file or directory
#include
^~~~~~~~~~~~~~~~~~
compilation terminated.
configure:3041: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME “rJava”
| #define PACKAGE_TARNAME “rjava”
| #define PACKAGE_VERSION “0.8”
| #define PACKAGE_STRING “rJava 0.8”
| #define PACKAGE_BUGREPORT “Simon.Urbanek@r-project.org”
| #define PACKAGE_URL “”
| /* end confdefs.h. */
| #include
configure:3066: result: ccache /usr/local/opt/gcc/bin/gcc-7 -E
configure:3086: ccache /usr/local/opt/gcc/bin/gcc-7 -E conftest.c
configure:3086: $? = 0
configure:3100: ccache /usr/local/opt/gcc/bin/gcc-7 -E conftest.c
conftest.c:9:10: fatal error: ac_nonexistent.h: No such file or directory
#include
^~~~~~~~~~~~~~~~~~
compilation terminated.
….

any ideas? thanks anyways!

Just make sure what version of JDK do you have:

ls -la /Library/Java/JavaVirtualMachines/

or call

/usr/libexec/java_home -V

In case of JDK you should take a look here: http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html and download most recent one.

And make sure to open Info.plist file with an editor you like (e.g. vi, emacs, TextMate).

Take a look here: http://www.owsiak.org/?p=3718

BTW, you have a typo

JAVA=${JAVA_HOME/bin/java \

JAVA=${JAVA_HOME}/bin/java \

Thanks for spotting it!

Fixed

I got the same error as Luis after following the steps as well

Take a look here: http://www.owsiak.org/?p=3718

Hello,

I also got the same error message in R

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’

Die heruntergeladenen Quellpakete sind in
‘/private/var/folders/rb/tb9pmxkj5wn529v73bdfsh100000gn/T/RtmpMipMTt/downloaded_packages’
Warnmeldung:
In install.packages(“rJava”, type = “source”) :
Installation des Pakets ‘rJava’ hatte Exit-Status ungleich 0

Please, let me know if you find any solution. Thanks!

Take a look here: http://www.owsiak.org/?p=3718

Hi,

I am also getting 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 ‘/Users/slee/Library/R/3.4/library/rJava’
Warning in install.packages :
installation of package ‘rJava’ had non-zero exit status

Any update on how to solve this error? Thanks!

To be honest, it’s hard to say. I can’t reproduce this kind of issue. All I can say is that it works for me, and I am using version:

clang –version
Apple LLVM version 8.1.0 (clang-802.0.42)
Target: x86_64-apple-darwin16.5.0
Thread model: posix

It seems I can’t help you much here :(

Take a look here: http://www.owsiak.org/?p=3718 – this one should fix the issue

“cd /Library/Java/JavaVirtualMachines/jdk1.8.0_11.jdk/Contents
ln -s Home RHome
then, you need to export it as JAVA_HOME ”

I am following the same step by step instruction as you mentioned. But I get an error saying ” Permission denied” at the above step in creating Java home directory

You might need to use “sudo”

sudo ln -s Home RHome

Hi ,

Thanks for answering my previous question . However when I try to confifure rJava manually , I get the following 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.
“`

I think this is related to mixed JDKs – Apple’s and Oracle’s :( At least this was the issue in my case.
You need to make sure to create artificial name for JDK that is not “Home”.

Hi Michal,

I am struggling quite a lot with this Java mess… At least the good thing is that I have learned quite a lot for my Mac :)
I am hoping you can take a look and give some advice :) Thanks a lot!

Log:
https://drive.google.com/open?id=0B7wVlzNi44EUMkpBYWowdTcwaW8

Info.plist:
https://drive.google.com/open?id=0B7wVlzNi44EUXzNiNUE4b0p3YjQ

Regards,
Hristo

It’s hard to judge what exactly is the source of the issue here. I’d suggest to play with JAVA_HOME pointing to JRE. And, as you can see, your R configuration mixes two Java releases – one from Oracle and one from Apple.

Hi michal,

I’m having the same problem as pranathi about One or more JNI types, I think you already solved this in your tutorial by making the RHome instead of Home. So how do I make “artificial name for JDK that is not “Home”” again?

cd /Library/Java/JavaVirtualMachines/jdk1.8.0_11.jdk/Contents
ln -s Home RHome

Hi Michal

Thanks for the post

Unfortunatelly I’m stuck on this:

sudo R CMD javareconf \
> JAVA_HOME=${JAVA_HOME} \
> JAVA=${JAVA_HOME}/../bin/java \
> JAVAC=${JAVA_HOME}/../bin/javac \
> JAVAH=${JAVA_HOME}/../bin/javah \
> JAR=${JAVA_HOME}/../bin/jar \
> JAVA_LIBS=”-L${JAVA_HOME}/lib/server -ljvm” \
> JAVA_CPPFLAGS=”-I${JAVA_HOME}/../include -I${JAVA_HOME}/../include/darwin”
Password:
/Library/Frameworks/R.framework/Resources/bin/javareconf: line 66: -ljvm: command not found
/Library/Frameworks/R.framework/Resources/bin/javareconf: line 66: -I/jre/../include/darwin: No such file or directory
*** JAVA_HOME is not a valid path, ignoring
Java interpreter : /jre/../bin/java
/Library/Frameworks/R.framework/Resources/bin/javareconf: line 105: /jre/../bin/java: No such file or directory

*** Java interpreter doesn’t work properly.

iMac-de-Fernando:~ fernandovieira$ export JAVA_HOME=$(/usr/libexec/java_home -v 9.0.1)iMac-de-Fernando:~ fernandovieira$ sudo R CMD javareconf \> JAVA_HOME=${JAVA_HOME} \> JAVA=${JAVA_HOME}/../bin/java \
> JAVAC=${JAVA_HOME}/../bin/javac \
> JAVAH=${JAVA_HOME}/../bin/javah \
> JAR=${JAVA_HOME}/../bin/jar \
> JAVA_LIBS=”-L${JAVA_HOME}/lib/server -ljvm” \
> JAVA_CPPFLAGS=”-I${JAVA_HOME}/../include -I${JAVA_HOME}/../include/darwin”
Password:
/Library/Frameworks/R.framework/Resources/bin/javareconf: line 66: -ljvm: command not found
/Library/Frameworks/R.framework/Resources/bin/javareconf: line 66: -I/Library/Java/JavaVirtualMachines/jdk-9.0.1.jdk/Contents/Home/../include/darwin: No such file or directory
Java interpreter : /Library/Java/JavaVirtualMachines/jdk-9.0.1.jdk/Contents/Home/../bin/java
/Library/Frameworks/R.framework/Resources/bin/javareconf: line 105: /Library/Java/JavaVirtualMachines/jdk-9.0.1.jdk/Contents/Home/../bin/java: No such file or directory

*** Java interpreter doesn’t work properly.

Could you help me?

It looks like Java 9 changed the layout (they have separated JRE and JDK completely). I will get back to this article and prepare something like: “R 3.4, JDK 9 and super mess in macOS”. Stay tuned.

Michal and Luis, when starting to run Luis’ solution, I got the following message:

Last login: Sat Jan 6 18:23:21 on ttys000
Gilvans-MBP:~ grguedes$ mkdir ~/opt
Gilvans-MBP:~ grguedes$ cd ~/opt
Gilvans-MBP:opt grguedes$ curl http://releases.llvm.org/4.0.1/clang+llvm-4.0.1-x86_64-apple-darwin.tar.xz \
> -o clang+llvm-4.0.1-x86_64-apple-darwin.tar.xz
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 –:–:– 0:00:22 –:–:– 0
100 447 100 447 0 0 7 0 0:01:03 0:01:02 0:00:01 130
Gilvans-MBP:opt grguedes$
Gilvans-MBP:opt grguedes$ tar xf clang+llvm-4.0.1-x86_64-apple-darwin.tar.xz
tar: Unrecognized archive format
tar: Error exit delayed from previous errors.
Gilvans-MBP:opt grguedes$

Where is the problem?
Thank you!

Try this one instead:

curl -O http://releases.llvm.org/4.0.1/clang+llvm-4.0.1-x86_64-apple-darwin.tar.xz

From the size of your download it looks like there were some problems while accessing file. You can check it by calling:

cat clang+llvm-4.0.1-x86_64-apple-darwin.tar.xz

Hello

when i try to start rjava i get the following error

Fehler: package or namespace load failed for ‘rJava’:
.onLoad in loadNamespace() für ‘rJava’ fehlgeschlagen, Details:
Aufruf: dyn.load(file, DLLpath = DLLpath, …)
Fehler: kann shared object ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava/libs/rJava.so’ nicht laden:
dlopen(/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava/libs/rJava.so, 6): Library not loaded: @rpath/libjvm.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava/libs/rJava.so
Reason: image not found

I tried to step through the workaround but i also ended up with this error

manuelkühnle-pc:~ MOK$ sudo R CMD javareconf
Password:
Java interpreter : /usr/bin/java
Java version : 1.6.0_65
Java home path : /Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home
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 :
detected JNI linker flags : -L/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Libraries -ljvm
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c conftest.c -o conftest.o
conftest.c:1:10: fatal error: ‘jni.h’ file not found
#include
^
1 error generated.
make: *** [conftest.o] Error 1
Unable to compile a JNI program

JAVA_HOME : /Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home
Java library path:
JNI cpp flags :
JNI linker flags :
Updating Java configuration in /Library/Frameworks/R.framework/Resources
Done.

Can anybody help please

It looks like your R configuration mixes two Java installations. Apple’s one and Oracle’s one.

Have you tried to do this trick?

cd /Library/Java/JavaVirtualMachines/jdk1.8.0_11.jdk/Contents
ln -s Home RHome

Have followed all steps above bu I get some errors both when I install and try to load rJava. No clue how to fix or even what is wrong..

library(rJava)
Error : .onLoad failed in loadNamespace() for ‘rJava’, details:
call: dyn.load(file, DLLpath = DLLpath, …)
error: unable to load shared object ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/rJava/libs/rJava.so’:
dlopen(/Library/Frameworks/R.framework/Versions/3.3/Resources/library/rJava/libs/rJava.so, 6): Library not loaded: @rpath/libjvm.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/3.3/Resources/library/rJava/libs/rJava.so
Reason: image not found
Error: package or namespace load failed for ‘rJava’

during installation from source I get these warnings:
>clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I/Library/Java/JavaVirtualMachines/jdk1.8.0_161.jdk/Contents/RHome/include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_161.jdk/Contents/RHome/include/darwin -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c Rglue.c -o Rglue.o
Rglue.c:847:13: warning: unused function ‘new_jrectRef’ [-Wunused-function]
static SEXP new_jrectRef(JNIEnv *env, jobject a, const char *sig, SEXP dim ) {
^
1 warning generated.

>/Library/Java/JavaVirtualMachines/jdk1.8.0_161.jdk/Contents/RHome/bin/javac -target 1.6 -source 1.6 -d . ../Mutex.java ../RBool.java ../RConsoleOutputStream.java ../REXP.java ../RFactor.java ../RList.java ../RMainLoopCallbacks.java ../RVector.java ../Rengine.java ../package-info.java
warning: [options] bootstrap class path not set in conjunction with -source 1.6
Note: Some input files use unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
1 warning

>/Library/Java/JavaVirtualMachines/jdk1.8.0_161.jdk/Contents/RHome/bin/javac -target 1.6 -source 1.6 -d . ../Mutex.java ../RBool.java ../RConsoleOutputStream.java ../REXP.java ../RFactor.java ../RList.java ../RMainLoopCallbacks.java ../RVector.java ../Rengine.java ../package-info.java
warning: [options] bootstrap class path not set in conjunction with -source 1.6
Note: Some input files use unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
1 warning

>/Library/Java/JavaVirtualMachines/jdk1.8.0_161.jdk/Contents/RHome/bin/javac -target 1.6 -source 1.6 -classpath src/JRI.jar -d examples examples/rtest.java
warning: [options] bootstrap class path not set in conjunction with -source 1.6
Note: examples/rtest.java uses or overrides a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
1 warning

>/Library/Java/JavaVirtualMachines/jdk1.8.0_161.jdk/Contents/RHome/bin/javac -target 1.6 -source 1.6 -classpath src/JRI.jar -d examples examples/rtest2.java
warning: [options] bootstrap class path not set in conjunction with -source 1.6
Note: examples/rtest2.java uses or overrides a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
1 warning

Here is my javareconf output:
sudo R CMD javareconf
Java interpreter : /usr/bin/java
Java version : 1.8.0_161
Java home path : /Library/Java/JavaVirtualMachines/jdk1.8.0_161.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_161.jdk/Contents/Home/jre/../include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_161.jdk/Contents/Home/jre/../include/darwin -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -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_161.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_161.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
Done.

Strange, it looks like you have mixed Linux/macOS env. Strange, that your system is looking for so files (they are common for Linux).

Yes, very strange and no clue how I ended up in this place…

I did however manage to get it working (I think) via a total random walk through the interwebs.

It ended with me noticing that I was able to load rJava in a session launched in terminal but not through the r.app-interface. In a standard R-session however I could only ger rJava to load after having manually loaded the libjvm.dylib that is mentioned in the load-error in R (@rpath/libjvm.dylib).

After manual load the code below spit out both the installed java version info as well as the allocated memory.

dyn.load(‘/Library/Java/JavaVirtualMachines/jdk1.8.0_161.jdk/Contents/Home/jre/lib/server/libjvm.dylib’)
options( java.parameters = “-Xmx4g” )
library(rJava)

.jinit()
.jcall(“java/lang/System”, “S”, “getProperty”, “java.runtime.version”)

library( “RBioFormats” )
checkJavaMemory()

Thanks for taking the time to write this up. Incredibly helpful

Thanks !!

Worked for me on OS X 10.13.4 with fresh jdk-10.0.1.jdk install and rJava_0.9-9
jdk-10.0.1 is my only JVM (singular output of /usr/libexec/java_home -V)
I did not have to edit /usr/libexec/java_home`/../Info.plist

Thanks!

Cool!