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

[Berend Hasselman]

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