> 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