> On 14 Feb 2016, at 23:13, Simon Urbanek <simon.urba...@r-project.org> wrote: > > Check DYLD_FALLBACK_LIBRARY_PATH - it must include your Java: > >> Sys.getenv("DYLD_FALLBACK_LIBRARY_PATH") > [1] > "/Library/Frameworks/R.framework/Resources/lib:/Library/Java/JavaVirtualMachines/jdk1.8.0_20.jdk/Contents/Home/jre/lib/server" > > if it doesn't, your R is not correctly configured. Oracle's Java requires the > above setting, it doesn't work without it (unlike the system Java). The above > is set by the R script based on etc/ldpaths - so make sure that one is > correct (it should be by javareconf if your system is setup correctly). >
Thanks; this lead to resolving the problem. I should have mentioned I was using library(rJava) and the others in the GUI R.app. In Terminal R shows > Sys.getenv("DYLD_FALLBACK_LIBRARY_PATH") [1] "/Library/Frameworks/R.framework/Resources/lib:/Library/Java/JavaVirtualMachines/jdk1.8.0_74.jdk/Contents/Home/jre/lib/server" as required. I've had to compile rJava from source as suggested by Brian Ripley (if I use the binary on CRAN I get errors)(on OS X 10.11.3). I've installed the binaries of XLConnect, etc. I can now run things like XLConnect from R in the Terminal and from bash scripts. I can't run anything using rJava in the GUI R.app or in Rstudio. BTW. R.app ([R.app GUI 1.67 (7129) x86_64-apple-darwin13.4.0]) shows > Sys.getenv("DYLD_FALLBACK_LIBRARY_PATH") [1] "" and Rstudio (Version 0.99.878) shows this > Sys.getenv("DYLD_FALLBACK_LIBRARY_PATH") [1] "/Library/Frameworks/R.framework/Resources/lib:/Users/berendhasselman/lib:/usr/local/lib:/usr/lib::" Where it got "/Users/berendhasselman/lib" from I wouldn't know; the folder does not exist. thanks a lot Berend > Cheers, > Simon > > > On Feb 14, 2016, at 6:47 AM, Berend Hasselman <b...@xs4all.nl> wrote: > >> >>> On 14 Feb 2016, at 12:31, Prof Brian Ripley <rip...@stats.ox.ac.uk> wrote: >>> >>> On 14/02/2016 11:24, Berend Hasselman wrote: >>>> >>>>> On 14 Feb 2016, at 11:48, Prof Brian Ripley <rip...@stats.ox.ac.uk> wrote: >>>>> >>>>> Your Java is seriously old. Start by updating it (1.8.0_74 is current, >>>>> AFAIK). >>>>> >>>>> I can reproduce this with the CRAN binary packages, but installing the >>>>> packages from source works for me on El Capitan (using the CRAN binary >>>>> R). So I suspect a problem with the CRAN binary package of rJava, which >>>>> seems to be hard-coded to use /System/Library/Frameworks/JavaVM.framework >>>>> and not Oracle Java. >>>>> >>>> >>>> I've just updated to Java 1.8.0_74. >>>> I get the same issues. >>>> >>>> >>>> And I have now also installed rJava, XLConnect end XLConnectJars from >>>> source. >>>> library(XLConnect) gives this error >>>> >>>> <message> >>>> Loading required package: XLConnectJars >>>> Error : .onLoad failed in loadNamespace() for 'rJava', details: >>>> call: dyn.load(file, DLLpath = DLLpath, ...) >>>> error: unable to load shared object >>>> '/Users/berendhasselman/Library/R/3.2/library/rJava/libs/rJava.so': >>>> dlopen(/Users/berendhasselman/Library/R/3.2/library/rJava/libs/rJava.so, >>>> 6): Library not loaded: @rpath/libjvm.dylib >>>> Referenced from: >>>> /Users/berendhasselman/Library/R/3.2/library/rJava/libs/rJava.so >>>> Reason: image not found >>>> Error: package 'XLConnectJars' could not be loaded >>>> </message> >>>> >>>> Apparently rJava.so can't be found. But I had already installed it from >>>> source. >>> >>> That is not what the message says ... it is libjvm which is not being found. >>> >> >> Correct. Sorry about that. >> >>> Did you re-run R CMD javareconf? (You might need to reinstall rJava from >>> source once you do.) >>> >> >> Yes I did and have done so again. I've reinstalled rJava from source and get >> the same error and the same output of running otool -L on rJava.so. >> >> Berend >> >> Output of R CMD javareconf: >> >> Java interpreter : /usr/bin/java >> Java version : 1.8.0_74 >> Java home path : >> /Library/Java/JavaVirtualMachines/jdk1.8.0_74.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/jdk1.8.0_74.jdk/Contents/Home/jre/../include >> >> -I/Library/Java/JavaVirtualMachines/jdk1.8.0_74.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/jdk1.8.0_74.jdk/Contents/Home/jre/lib/server >> -ljvm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework >> -Wl,CoreFoundation >> >> >> JAVA_HOME : >> /Library/Java/JavaVirtualMachines/jdk1.8.0_74.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. >> >> >> >>> >>>> I have run otool on the installed rJava.so >>>> >>>> otool -L rJava.so >>>> rJava.so: >>>> rJava.so (compatibility version 0.0.0, current version 0.0.0) >>>> @rpath/libjvm.dylib (compatibility version 1.0.0, current version 1.0.0) >>>> /Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libR.dylib >>>> (compatibility version 3.2.0, current version 3.2.3) >>>> >>>> /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation >>>> (compatibility version 150.0.0, current version 1256.14.0) >>>> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current >>>> version 1226.10.1) >>>> >>>> Berend >>>> >>>>> On 14/02/2016 09:22, Berend Hasselman wrote: >>>>>> I have installed rJava, xlsx, xlsxjars, XLConnect and XLConnectJars. >>>>>> >>>>>> Executing library(xlsx) gives this output >>>>>> >>>>>> Loading required package: rJava >>>>>> Loading required package: xlsxjars >>>>>> Error : .onLoad failed in loadNamespace() for 'xlsx', details: >>>>>> call: .jinit() >>>>>> error: JNI_GetCreatedJavaVMs returned -1 >>>>>> >>>>>> Error: package or namespace load failed for 'xlsx' >>>>>> 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. >>>>>> >>>>>> >>>>>> Executing library(XLConnect) gives this output >>>>>> >>>>>> Loading required package: XLConnectJars >>>>>> Error : .onLoad failed in loadNamespace() for 'XLConnectJars', details: >>>>>> call: .jinit() >>>>>> error: JNI_GetCreatedJavaVMs returned -1 >>>>>> >>>>>> Error: package 'XLConnectJars' could not be loaded >>>>>> 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. >>>>>> >>>>>> >>>>>> sessionInfo (after library(xlsx) and library(XLConnect)) and javareconf >>>>>> output below. >>>>>> >>>>>> What is going on? >>>>>> What is the solution for this problem? >>>>>> >>>>>> Berend Hasselman >>>>>> >>>>>> >>>>>> SessionInfo: >>>>>> >>>>>> R version 3.2.3 Patched (2016-02-13 r70160) >>>>>> Platform: x86_64-apple-darwin13.4.0 (64-bit) >>>>>> Running under: OS X 10.11.3 (El Capitan) >>>>>> >>>>>> locale: >>>>>> [1] en_IE.UTF-8/en_IE.UTF-8/en_IE.UTF-8/C/en_IE.UTF-8/en_IE.UTF-8 >>>>>> >>>>>> attached base packages: >>>>>> [1] stats graphics grDevices utils datasets methods base >>>>>> >>>>>> other attached packages: >>>>>> [1] xlsxjars_0.6.1 rJava_0.9-8 >>>>>> >>>>>> loaded via a namespace (and not attached): >>>>>> [1] tools_3.2.3 >>>>>> >>>>>> >>>>>> Output of R CMD javareconf >>>>>> >>>>>> [.../~]: R CMD javareconf -n >>>>>> Java interpreter : /usr/bin/java >>>>>> Java version : 1.8.0_25 >>>>>> Java home path : >>>>>> /Library/Java/JavaVirtualMachines/jdk1.8.0_25.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/jdk1.8.0_25.jdk/Contents/Home/jre/../include >>>>>> >>>>>> -I/Library/Java/JavaVirtualMachines/jdk1.8.0_25.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/jdk1.8.0_25.jdk/Contents/Home/jre/lib/server >>>>>> -ljvm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework >>>>>> -Wl,CoreFoundation >>>>>> >>>>>> JAVA_HOME : >>>>>> /Library/Java/JavaVirtualMachines/jdk1.8.0_25.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 >>>>>> >>>>>> _______________________________________________ >>>>>> R-SIG-Mac mailing list >>>>>> R-SIG-Mac@r-project.org >>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >>>>>> >>>>> >>>>> >>>>> -- >>>>> Brian D. Ripley, rip...@stats.ox.ac.uk >>>>> Emeritus Professor of Applied Statistics, University of Oxford >>>> >>> >>> >>> -- >>> Brian D. Ripley, rip...@stats.ox.ac.uk >>> Emeritus Professor of Applied Statistics, University of Oxford >> >> _______________________________________________ >> 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