Berend, I now have working packages, thanks!
The key was installing rJava from source rather than binary (binary being the default when using install.packages(); I had already run javareconf so there was no change there). And apologies to everyone for failing to search hard enough to find the solution that was already available on R-sig-mac. As an aside, yes, my Java is indeed old, but my institution, for whatever reason, is not offering a more recent version in its software deployment system. -Don Don MacQueen Lawrence Livermore National Laboratory macque...@llnl.gov 925-423-1062 > On Jun 18, 2016, at 12:43 AM, Berend Hasselman <b...@xs4all.nl> wrote: > > >> On 18 Jun 2016, at 00:28, MacQueen, Don <macque...@llnl.gov> 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 >> 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 > _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
