> On 18 Jun 2016, at 00:28, MacQueen, Don <[email protected]> wrote: > > 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. >
I had similar issues with rJava. See this thread: https://stat.ethz.ch/pipermail/r-sig-mac/2016-February/011836.html I made a shell script for reinstalling rJava whenever the R version changes. It runs in the folder where you have the rJava source tarball. <script> R -e 'Sys.getenv("DYLD_FALLBACK_LIBRARY_PATH")' R CMD javareconf R -e 'Sys.getenv("DYLD_FALLBACK_LIBRARY_PATH")' RMAINLIB="$(R RHOME)/library" # install rJava from source in to main library R CMD INSTALL --library="$RMAINLIB" rJava_0.9-8.tar.gz > install.out </script> I've just tested this after removing the installed version of rJava. I can load things like XLConnect etc. without problems. Then you can use rJava etc. with R in Terminal. Using rJava doesn't work in/with R GUI. Berend > -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 > [email protected] > 925-423-1062 > > > > _______________________________________________ > R-SIG-Mac mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/r-sig-mac _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
