> On Jun 18, 2016, at 4:32 AM, Charles DiMaggio <charles.dimag...@gmail.com> > wrote: > > Recently came up against the same issue with package �RNetLogo�, so appears > to not be an isolated issue. Solution for me was to > > (1) ensure latest version of java (type "java -version" without the quotes in > your terminal), if less than 1.8, install Java SE Development Kit 8u91 > (http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html) > and > > (2) run the program through JGR. I needed to tweak the settings a bit when > running JGR: > > Sys.setenv(NOAWT=1) > library(JGR) > Sys.unsetenv("NOAWT") > JGR() > > Wasn�t entirely happy about having to leave my preferred editor (Textmate), > but it worked. > > Cheers > > Charles > Charles DiMaggio, PhD, MPH > Professor of Surgery and Population Health >
I recently had failure on an El Capitan machine running R 3.3.0 RC to load pkg:XLConnect and got identical message attempting to load pkg:xlsx. #------------ > library(XLConnect) Loading required package: XLConnectJars Error : .onLoad failed in loadNamespace() for 'rJava', details: call: dyn.load(file, DLLpath = DLLpath, ...) error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.3/Resources/library/rJava/libs/rJava.so': dlopen(/Library/Frameworks/R.framework/Versions/3.3/Resources/library/rJava/libs/rJava.so, 6): Library not loaded: @rpath/libjvm.dylib Referenced from: /Library/Frameworks/R.framework/Versions/3.3/Resources/library/rJava/libs/rJava.so Reason: image not found Error: package ‘XLConnectJars’ could not be loaded #------------ Searching StackOverflow I found an answer that reported success with this system level incantation: david-winsemiuss-mac-pro:~ davidwinsemius$ sudo ln -s $(/usr/libexec/java_home)/jre/lib/server/libjvm.dylib /usr/local/lib Password: # I (think) this creates a link to the current libjvm in the "newly blessed" OSX library location under the tightened OSX rules of user engagement. Then success with both packages loading. Now get: $ java -version java version "1.8.0_65" Java(TM) SE Runtime Environment (build 1.8.0_65-b17) Java HotSpot(™) 64-Bit Server VM (build 25.65-b01, mixed mode) I didn't know if my R sessions would have the same result, since I had both a 1.6 which I thought was the designated Java version for R, and a 1.8 version of the Java RTE, but seems I'm now simply using 1.8. > system("java -version") java version "1.8.0_65" Java(TM) SE Runtime Environment (build 1.8.0_65-b17) Java HotSpot(™) 64-Bit Server VM (build 25.65-b01, mixed mode) > > On Jun 18, 2016, at 3:43 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 > > > [[alternative HTML version deleted]] > > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac David Winsemius Alameda, CA, USA _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac