[R-SIG-Mac] Issues with rJava on OS X El Capitan

[Prof Brian Ripley]

On 14/02/2016 11:24, Berend Hasselman wrote:
>
>> On 14 Feb 2016, at 11:48, Prof Brian Ripley <ripley at stats.ox.ac.uk> wrote:
>>
>> Your Java is seriously old.  Start by updating it (1.8.0_74 is current, AFAIK).
>>
>> I can reproduce this with the CRAN binary packages, but installing the packages from source works for me on El Capitan (using the CRAN binary R).  So I suspect a problem with the CRAN binary package of rJava, which seems to be hard-coded to use /System/Library/Frameworks/JavaVM.framework and not Oracle Java.
>>
>
> I've just updated to Java 1.8.0_74.
> I get the same issues.
>
>
> And I have now also installed rJava, XLConnect end XLConnectJars from source.
> library(XLConnect) gives this error
>
> <message>
> Loading required package: XLConnectJars
> Error : .onLoad failed in loadNamespace() for 'rJava', details:
>    call: dyn.load(file, DLLpath = DLLpath, ...)
>    error: unable to load shared object '/Users/berendhasselman/Library/R/3.2/library/rJava/libs/rJava.so':
>    dlopen(/Users/berendhasselman/Library/R/3.2/library/rJava/libs/rJava.so, 6): Library not loaded: @rpath/libjvm.dylib
>    Referenced from: /Users/berendhasselman/Library/R/3.2/library/rJava/libs/rJava.so
>    Reason: image not found
> Error: package 'XLConnectJars' could not be loaded
> </message>
>
> Apparently rJava.so can't be found. But I had already installed it from source.

That is not what the message says ... it is libjvm which is not being found.

Did you re-run R CMD javareconf?  (You might need to reinstall rJava 
from source once you do.)



> I have run otool on the installed rJava.so
>
> otool -L rJava.so
> rJava.so:
> 	rJava.so (compatibility version 0.0.0, current version 0.0.0)
> 	@rpath/libjvm.dylib (compatibility version 1.0.0, current version 1.0.0)
> 	/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libR.dylib (compatibility version 3.2.0, current version 3.2.3)
> 	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1256.14.0)
> 	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1226.10.1)
>
> Berend
>
>> On 14/02/2016 09:22, Berend Hasselman wrote:
>>> I have installed rJava, xlsx, xlsxjars, XLConnect and XLConnectJars.
>>>
>>> Executing library(xlsx) gives this output
>>>
>>> Loading required package: rJava
>>> Loading required package: xlsxjars
>>> Error : .onLoad failed in loadNamespace() for 'xlsx', details:
>>>    call: .jinit()
>>>    error: JNI_GetCreatedJavaVMs returned -1
>>>
>>> Error: package or namespace load failed for 'xlsx'
>>> JavaVM: requested Java version ((null)) not available. Using Java at "" instead.
>>> JavaVM: Failed to load JVM: /bundle/Libraries/libserver.dylib
>>> JavaVM FATAL: Failed to load the jvm library.
>>>
>>>
>>> Executing library(XLConnect) gives this output
>>>
>>> Loading required package: XLConnectJars
>>> Error : .onLoad failed in loadNamespace() for 'XLConnectJars', details:
>>>    call: .jinit()
>>>    error: JNI_GetCreatedJavaVMs returned -1
>>>
>>> Error: package 'XLConnectJars' could not be loaded
>>> JavaVM: requested Java version ((null)) not available. Using Java at "" instead.
>>> JavaVM: Failed to load JVM: /bundle/Libraries/libserver.dylib
>>> JavaVM FATAL: Failed to load the jvm library.
>>>
>>>
>>> sessionInfo (after library(xlsx) and library(XLConnect)) and javareconf output below.
>>>
>>> What is going on?
>>> What is the solution for this problem?
>>>
>>> Berend Hasselman
>>>
>>>
>>> SessionInfo:
>>>
>>> R version 3.2.3 Patched (2016-02-13 r70160)
>>> Platform: x86_64-apple-darwin13.4.0 (64-bit)
>>> Running under: OS X 10.11.3 (El Capitan)
>>>
>>> locale:
>>> [1] en_IE.UTF-8/en_IE.UTF-8/en_IE.UTF-8/C/en_IE.UTF-8/en_IE.UTF-8
>>>
>>> attached base packages:
>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>
>>> other attached packages:
>>> [1] xlsxjars_0.6.1 rJava_0.9-8
>>>
>>> loaded via a namespace (and not attached):
>>> [1] tools_3.2.3
>>>
>>>
>>> Output of R CMD javareconf
>>>
>>> [.../~]: R CMD javareconf -n
>>> 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
>>> Non-system Java on OS X
>>>
>>> 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_25.jdk/Contents/Home/jre/../include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_25.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_25.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_25.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
>>>
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>>>
>>
>>
>> --
>> Brian D. Ripley,                  ripley at stats.ox.ac.uk
>> Emeritus Professor of Applied Statistics, University of Oxford
>


-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford