[R-SIG-Mac] Problem with RJDBC in OS X 10.11

[MacQueen, Don]

I’m not sure the best place to ask about this, so I’ll start here, since the problem appears to be configuring Java on a Mac to support R packages. Unfortunately, my understanding of how to configure and manage Java is essentially non-existent, so any suggestions would be much appreciated. 

I have a script using RJDBC that is working on a Mac running OS X 10.10.5. The same script, with the same JDBC .jar files from Oracle, is not working on an OS X 10.11.4 machine, as shown below. Other packages that depend on Java, such as xlsx, are not working either.

I have run R CMD javareconf to no avail (output below).

The software management system used by our IT department claims that "Oracle Java 1.7 SDK and JRE" are installed.

-Don


> jdbm <- JDBC('oracle.jdbc.OracleDriver', '/opt/ora11g/instantclient_11_2/ojdbc6.jar', "`")
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.
Error in .jinit(classPath) : JNI_GetCreatedJavaVMs returned -1

> sessionInfo()
R version 3.3.0 (2016-05-03)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.4 (El Capitan)

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] RJDBC_0.2-5 rJava_0.9-8 DBI_0.4-1  



[macqueen1-ml:~]% sudo R CMD javareconf

Java interpreter : /usr/bin/java
Java version     : 1.7.0_101
Java home path   : /Library/Java/JavaVirtualMachines/jdk1.7.0_101.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/jdk1.7.0_101.jdk/Contents/Home/jre/../include -I/Library/Java/JavaVirtualMachines/jdk1.7.0_101.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/jdk1.7.0_101.jdk/Contents/Home/jre/lib/server -ljvm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation


JAVA_HOME        : /Library/Java/JavaVirtualMachines/jdk1.7.0_101.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.


Also:
[macqueen1-ml:~]% java -version
java version "1.7.0_101"
Java(TM) SE Runtime Environment (build 1.7.0_101-b14)
Java HotSpot(TM) 64-Bit Server VM (build 24.101-b14, mixed mode)



Don MacQueen
Lawrence Livermore National Laboratory
macqueen1 at llnl.gov
925-423-1062