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> 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
>
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