"No Java runtime" error in OS X 10.10 using Oracle's 1.8.0 JVM

[serpico7456]

I've tried 3 different Macs running OS X 10.10, R 3.1.2, Java 1.8.0_25, and rJava 0.9-7. In all three cases rJava installs from source without error but after running .jinit(), fails to detect Java and prompts to install Java 6 from apple. Another researcher at my institution reports the same issue.

I've spent hours researching online, but haven't yet found a solution and tried various things like manually setting JAVA_HOME and LD_LIBRARY_PATH to no avail.

R CMD javareconf
Java interpreter : /usr/bin/java
Java version : 1.8.0_25
Java home path : /Library/Java/JavaVirtualMachines/jdk1.8.0_25.jdk/Contents/Home/jre
Java compiler : /usr/bin/javac
Java headers gen.: /usr/bin/javah
Java archive tool: /usr/bin/jar
...

~ % echo $JAVA_HOME
/Library/Java/JavaVirtualMachines/jdk1.8.0_25.jdk/Contents/Home/jre
~ % echo $LD_LIBRARY_PATH
/Library/Java/JavaVirtualMachines/jdk1.8.0_25.jdk/Contents/Home/jre/lib/server

~ % R CMD INSTALL rJava_0.9-7.tar.gz

full compile output

~ % R

library('rJava')
.jinit()
No Java runtime present, requesting install.

[s-u]

I suspect this is something for Oracle support/lists, because rJava loads the correct JVM, but Oracle's code attempts to fall back to Apple Java or something like that:

> library(rJava)
dyld: loaded: /Library/Frameworks/R.framework/Versions/3.1/Resources/library/rJava/libs/rJava.so
dyld: loaded: /Library/Java/JavaVirtualMachines/jdk1.8.0_20.jdk/Contents/Home/jre/lib/server/libjvm.dylib
dyld: loaded: /usr/lib/libstdc++.6.dylib
> .jinit()
dyld: loaded: /Library/Java/JavaVirtualMachines/jdk1.8.0_20.jdk/Contents/Home/jre/lib/libverify.dylib
dyld: loaded: /Library/Java/JavaVirtualMachines/jdk1.8.0_20.jdk/Contents/Home/jre/lib/libjava.dylib
dyld: loaded: /Library/Java/JavaVirtualMachines/jdk1.8.0_20.jdk/Contents/Home/jre/lib/libzip.dylib
dyld: loaded: /System/Library/Frameworks/JavaVM.framework/Frameworks/JavaRuntimeSupport.framework/JavaRuntimeSupport
dyld: loaded: /System/Library/Frameworks/JavaVM.framework/Versions/A/Frameworks/JavaNativeFoundation.framework/Versions/A/JavaNativeFoundation
dyld: loaded: /System/Library/Frameworks/JavaVM.framework/Versions/A/JavaVM
dyld: loaded: /System/Library/Frameworks/Cocoa.framework/Versions/A/Cocoa
dyld: loaded: /System/Library/Frameworks/Carbon.framework/Versions/A/Carbon
dyld: loaded: /System/Library/PrivateFrameworks/JavaLaunching.framework/Versions/A/JavaLaunching
dyld: loaded: /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/CommonPanels.framework/Versions/A/CommonPanels
dyld: loaded: /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/Help.framework/Versions/A/Help
dyld: loaded: /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/ImageCapture.framework/Versions/A/ImageCapture
dyld: loaded: /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/OpenScripting.framework/Versions/A/OpenScripting
dyld: loaded: /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/Print.framework/Versions/A/Print
dyld: loaded: /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/SecurityHI.framework/Versions/A/SecurityHI
No Java runtime present, requesting install.

FWIW my javareconf is finding the full JDK correctly without any overrides:

$ R CMD javareconf -n
Java interpreter : /Library/Java/JavaVirtualMachines/jdk1.8.0_20.jdk/Contents/Home/bin/java
Java version     : 1.8.0_20
Java home path   : /Library/Java/JavaVirtualMachines/jdk1.8.0_20.jdk/Contents/Home/jre
Java compiler    : /Library/Java/JavaVirtualMachines/jdk1.8.0_20.jdk/Contents/Home/bin/javac
Java headers gen.: /Library/Java/JavaVirtualMachines/jdk1.8.0_20.jdk/Contents/Home/bin/javah
Java archive tool: /Library/Java/JavaVirtualMachines/jdk1.8.0_20.jdk/Contents/Home/bin/jar
Non-system Java on OS X

trying to compile and link a JNI progam 
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_20.jdk/Contents/Home/jre/../include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_20.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_20.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_20.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

[s-u]

Ok, this is officially a Java 1.8 bug:

https://bugs.openjdk.java.net/browse/JDK-7131356

Ironically, you have to install 1.6 from Apple

http://support.apple.com/kb/DL1572

then Oracle Java 1.8 will start working.

[sdaza]

But R still will use Java 6:

 library(rJava)  
 .jinit()
 .jcall("java/lang/System", "S", "getProperty", "java.runtime.version")
 [1] "1.6.0_65-b14-466.1-11M4716"

I need R uses Java 8 in order to use RNetLogo :(

[s-u]

Nope, if you link it against 1.8:

> library(rJava)
> .jinit()
> .jcall("java/lang/System", "S", "getProperty", "java.runtime.version")
[1] "1.8.0_20-b26"

This is with the config above.

1.8 needs the presence of 1.6, it will still correctly load the 1.8 JVM but due to the bug described above it makes a call to the system that will trip the 1.6 detection so the 1.8 JNI only works if 1.6 is installed.

[s-u]

If in doubt, check with DYLD_PRINT_LIBRARIES=1 (that's what the above output shows) to make sure you have linked rJava against 1.8 and not 1.6. If you have the wrong one either re-configure R (like I did above) or for a quick fix use install_name_tool on rJava.so to pick whichever libjvm you need.

[conjugateprior]

Hmm. Installed Oracle Java 1.8 (it works). Installed Java 1.6 from Apple (it gets picked up by rJava). Recofingured R via sudo R CMD javareconf -n (gives a lot of information about how it's using 1.8).

But then

library(rJava)
.jinit()
.jcall("java/lang/System", "S", "getProperty", "java.runtime.version")
[1] "1.6.0_65-b14-466.1-11M4716"

So I guess reconfiguration is not working.

[s-u]

Like I said, check which one you linked against (otool -L) and which libjvm you're loading.

[sdaza]

Great! Now it is working on my laptop :)

[s-u]

@conjugateprior to clarify - after re-configuring R you still have to re-compile rJava to pick up the new R settings

[conjugateprior]

Aha. I'd already re-installed as binary, but install.packages('rJava', type='source') seems to have done the trick.

.jcall("java/lang/System", "S", "getProperty", "java.runtime.version")
[1] "1.8.0_05-b13"

[yufree]

Hi, I tried @conjugateprior 's method(re-config R and rJava) and it still show me 1.6.0_65-b14-466.1-11M4716. When I use JGR, the issue disappeared. I am still confused but right now I could use RNetLogo.

[conjugateprior]

@yufree I've put as much as I understand in a blog post. The comments also have some detail on setting paths. I suppose it's possible that JGR is setting them correctly for you when loaded. (I've never used it, so I don't know.)

[yufree]

Thank you! I checked you posts and tried again in RStudio, still 1.6, not 1.8. It seemed something wired happened between RStudio and rJava.