I am encountering the same issue here, but when I got a different result as
below, what should I do for the next?
> Sys.getenv("DYLD_FALLBACK_LIBRARY_PATH")
[1]
"/Library/Frameworks/R.framework/Resources/lib:/Users/eileen/lib:/usr/local/lib:/usr/lib::"
Thanks,
Eileen
On Monday, February 15, 2016 at 6:15:04 AM UTC+8, Simon Urbanek 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).
>
> Cheers,
> Simon
>
>
> On Feb 14, 2016, at 6:47 AM, Berend Hasselman <b...@xs4all.nl
> <javascript:>> wrote:
>
> >
> >> On 14 Feb 2016, at 12:31, Prof Brian Ripley <rip...@stats.ox.ac.uk
> <javascript:>> 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
> <javascript:>> 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-si...@r-project.org <javascript:>
> >>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >>>>>
> >>>>
> >>>>
> >>>> --
> >>>> Brian D. Ripley, rip...@stats.ox.ac.uk <javascript:>
> >>>> Emeritus Professor of Applied Statistics, University of Oxford
> >>>
> >>
> >>
> >> --
> >> Brian D. Ripley, rip...@stats.ox.ac.uk <javascript:>
> >> Emeritus Professor of Applied Statistics, University of Oxford
> >
> > _______________________________________________
> > R-SIG-Mac mailing list
> > r-si...@r-project.org <javascript:>
> > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >
>
> _______________________________________________
> R-SIG-Mac mailing list
> r-si...@r-project.org <javascript:>
> 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
