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 macque...@llnl.gov 925-423-1062 _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac