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

[Berend Hasselman]

> 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.
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