[R-SIG-Mac] rJava stops loading since I upgraded R to 3.4.0

David Winsemius dwinsemius at comcast.net
Wed May 24 17:19:57 CEST 2017


> On May 24, 2017, at 7:40 AM, Christofer Bogaso <bogaso.christofer at gmail.com> wrote:
> 
> Hi,
> 
> I have installed javac to it's latest version, still the problem
> persists. Below is the latest result
> 
>> library(rJava)
> 
> Error: package or namespace load failed for ‘rJava’:
> 
> .onLoad failed in loadNamespace() for 'rJava', details:
> 
>  call: dyn.load(file, DLLpath = DLLpath, ...)
> 
>  error: unable to load shared object
> '/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava/libs/rJava.so':
> 
>  dlopen(/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava/libs/rJava.so,
> 6): Library not loaded: @rpath/libjvm.dylib
> 
>  Referenced from:
> /Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava/libs/rJava.so
> 
>  Reason: image not found
> 
>> file.exists('/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava/libs/rJava.so')
> 
> [1] TRUE
> 
>> system('javac -version')
> 
> javac 1.8.0_131
> 
> 
> Also, when I ran 'sudo R CMD javareconf' in my Terminal, I got below result :
> 
> dyld: Library not loaded:
> @rpath/DVTFoundation.framework/Versions/A/DVTFoundation
> 
>  Referenced from: /Applications/Xcode.app/Contents/Developer/usr/bin/xcodebuild
> 
>  Reason: no suitable image found.  Did find:
> 
> /Applications/Xcode.app/Contents/Developer/usr/bin/../../../SharedFrameworks/DVTFoundation.framework/Versions/A/DVTFoundation:
> cannot load '/Applications/Xcode.app/Contents/Developer/usr/bin/../../../SharedFrameworks/DVTFoundation.framework/Versions/A/DVTFoundation'
> because Objective-C garbage collection is not supported
> 
> xcrun: error: unable to locate xcodebuild, please make sure the path
> to the Xcode folder is set correctly!
> 
> xcrun: error: You can set the path to the Xcode folder using
> /usr/bin/xcode-select -switch

So did you follow the advice in the error messages? I interpret this to suggest you didn't update Xcode when you updated to Sierra.

-- 
David.


> 
> dyld: Library not loaded:
> @rpath/DVTFoundation.framework/Versions/A/DVTFoundation
> 
>  Referenced from: /Applications/Xcode.app/Contents/Developer/usr/bin/xcodebuild
> 
>  Reason: no suitable image found.  Did find:
> 
> /Applications/Xcode.app/Contents/Developer/usr/bin/../../../SharedFrameworks/DVTFoundation.framework/Versions/A/DVTFoundation:
> cannot load '/Applications/Xcode.app/Contents/Developer/usr/bin/../../../SharedFrameworks/DVTFoundation.framework/Versions/A/DVTFoundation'
> because Objective-C garbage collection is not supported
> 
> xcrun: error: unable to locate xcodebuild, please make sure the path
> to the Xcode folder is set correctly!
> 
> xcrun: error: You can set the path to the Xcode folder using
> /usr/bin/xcode-select -switch
> 
> dyld: Library not loaded:
> @rpath/DVTFoundation.framework/Versions/A/DVTFoundation
> 
>  Referenced from: /Applications/Xcode.app/Contents/Developer/usr/bin/xcodebuild
> 
>  Reason: no suitable image found.  Did find:
> 
> /Applications/Xcode.app/Contents/Developer/usr/bin/../../../SharedFrameworks/DVTFoundation.framework/Versions/A/DVTFoundation:
> cannot load '/Applications/Xcode.app/Contents/Developer/usr/bin/../../../SharedFrameworks/DVTFoundation.framework/Versions/A/DVTFoundation'
> because Objective-C garbage collection is not supported
> 
> xcrun: error: unable to locate xcodebuild, please make sure the path
> to the Xcode folder is set correctly!
> 
> xcrun: error: You can set the path to the Xcode folder using
> /usr/bin/xcode-select -switch
> 
> dyld: Library not loaded:
> @rpath/DVTFoundation.framework/Versions/A/DVTFoundation
> 
>  Referenced from: /Applications/Xcode.app/Contents/Developer/usr/bin/xcodebuild
> 
>  Reason: no suitable image found.  Did find:
> 
> /Applications/Xcode.app/Contents/Developer/usr/bin/../../../SharedFrameworks/DVTFoundation.framework/Versions/A/DVTFoundation:
> cannot load '/Applications/Xcode.app/Contents/Developer/usr/bin/../../../SharedFrameworks/DVTFoundation.framework/Versions/A/DVTFoundation'
> because Objective-C garbage collection is not supported
> 
> xcrun: error: unable to locate xcodebuild, please make sure the path
> to the Xcode folder is set correctly!
> 
> xcrun: error: You can set the path to the Xcode folder using
> /usr/bin/xcode-select -switch
> 
> dyld: Library not loaded:
> @rpath/DVTFoundation.framework/Versions/A/DVTFoundation
> 
>  Referenced from: /Applications/Xcode.app/Contents/Developer/usr/bin/xcodebuild
> 
>  Reason: no suitable image found.  Did find:
> 
> /Applications/Xcode.app/Contents/Developer/usr/bin/../../../SharedFrameworks/DVTFoundation.framework/Versions/A/DVTFoundation:
> cannot load '/Applications/Xcode.app/Contents/Developer/usr/bin/../../../SharedFrameworks/DVTFoundation.framework/Versions/A/DVTFoundation'
> because Objective-C garbage collection is not supported
> 
> xcrun: error: unable to locate xcodebuild, please make sure the path
> to the Xcode folder is set correctly!
> 
> xcrun: error: You can set the path to the Xcode folder using
> /usr/bin/xcode-select -switch
> 
> dyld: Library not loaded:
> @rpath/DVTFoundation.framework/Versions/A/DVTFoundation
> 
>  Referenced from: /Applications/Xcode.app/Contents/Developer/usr/bin/xcodebuild
> 
>  Reason: no suitable image found.  Did find:
> 
> /Applications/Xcode.app/Contents/Developer/usr/bin/../../../SharedFrameworks/DVTFoundation.framework/Versions/A/DVTFoundation:
> cannot load '/Applications/Xcode.app/Contents/Developer/usr/bin/../../../SharedFrameworks/DVTFoundation.framework/Versions/A/DVTFoundation'
> because Objective-C garbage collection is not supported
> 
> xcrun: error: unable to locate xcodebuild, please make sure the path
> to the Xcode folder is set correctly!
> 
> xcrun: error: You can set the path to the Xcode folder using
> /usr/bin/xcode-select -switch
> 
> Java interpreter : /usr/bin/java
> 
> Java version     : 1.8.0_131
> 
> Java home path   :
> /Library/Java/JavaVirtualMachines/jdk1.8.0_131.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 macOS
> 
> 
> 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/Users/ARRUN/Library/Java/Extensions
> -L/Library/Java/Extensions -L/Network/Library/Java/Extensions
> -L/System/Library/Java/Extensions -L/usr/lib/java -L. -ljvm
> 
> dyld: Library not loaded:
> @rpath/DVTFoundation.framework/Versions/A/DVTFoundation
> 
>  Referenced from: /Applications/Xcode.app/Contents/Developer/usr/bin/xcodebuild
> 
>  Reason: no suitable image found.  Did find:
> 
> /Applications/Xcode.app/Contents/Developer/usr/bin/../../../SharedFrameworks/DVTFoundation.framework/Versions/A/DVTFoundation:
> cannot load '/Applications/Xcode.app/Contents/Developer/usr/bin/../../../SharedFrameworks/DVTFoundation.framework/Versions/A/DVTFoundation'
> because Objective-C garbage collection is not supported
> 
> xcrun: error: unable to locate xcodebuild, please make sure the path
> to the Xcode folder is set correctly!
> 
> xcrun: error: You can set the path to the Xcode folder using
> /usr/bin/xcode-select -switch
> 
> Unable to compile a JNI program
> 
> 
> 
> JAVA_HOME        :
> /Library/Java/JavaVirtualMachines/jdk1.8.0_131.jdk/Contents/Home/jre
> 
> Java library path:
> 
> JNI cpp flags    :
> 
> JNI linker flags :
> 
> Updating Java configuration in /Library/Frameworks/R.framework/Resources
> 
> Done.
> 
> On Wed, May 24, 2017 at 10:28 AM, Simon Urbanek
> <simon.urbanek at r-project.org> wrote:
>> Christofer,
>> 
>>> On May 23, 2017, at 7:44 PM, Christofer Bogaso <bogaso.christofer at gmail.com> wrote:
>>> 
>>> Hi David,
>>> 
>>> The file 'rJava.so' exists in my machine :
>>> 
>>>> file.exists('/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava/libs/rJava.so')
>>> 
>>> [1] TRUE
>>> 
>>> Also the Javac version that I have :
>>> 
>>>> system('javac -version')
>>> 
>>> javac 1.6.0_65
>>> 
>>> Looks like mine is older than you. Do I need to download the latest?
>>> In that case, do you suggest any link? As far as I know, javac comes
>>> with Mac installed.
>>> 
>> 
>> Apple has dropped Java support many years ago - what you have a is a left-over from a very old OS X version as you likely upgraded your OS X over the years without re-installing.
>> Since R 3.4.0 the CRAN binary uses Java 1.8, because too many users have complained about incompatibilities with old Java version, so you have two options
>> 1) recompile rJava from sources against your ancient Java
>> 2) install Java 1.8 from Oracle[1], then run R CMD javareconf
>> 
>> [1] http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html
>> 
>> Cheers,
>> Simon
>> 
>> 
>> 
>>> On Peter's suggestion I also did sudo R CMD javareconf. However still
>>> rJava couldnt be loaded.
>>> 
>>> Any other idea? Thanks,
>>> 
>>> On Wed, May 24, 2017 at 4:28 AM, peter dalgaard <pdalgd at gmail.com> wrote:
>>>> [Christofer seemed to have fallen off the cc: list, now included]
>>>> 
>>>>> On 24 May 2017, at 00:18 , David Winsemius <dwinsemius at comcast.net> wrote:
>>>>> 
>>>>> What version of the Java Runtime Environment is available? What do you get for:
>>>>> 
>>>>> system('javac -version')
>>>>> #I get:
>>>>> #javac 1.8.0_65
>>>>> 
>>>>> I think that version was working with rJava, but I followed the "critical" advice on the Java SDK webpage ...
>>>>> 
>>>>> ... and after updating I now  get
>>>>> #javac 1.8.0_131
>>>>> 
>>>>> And rJava still loads without error. I'm not on Sierra, however.
>>>>> 
>>>> 
>>>> I am, and rJava doesn't load here either. However after
>>>> 
>>>> sudo R CMD javareconf
>>>> 
>>>> it seems happy as a clam.
>>>> 
>>>> 
>>>>> Good luck;
>>>>> David,
>>>> 
>>>> --
>>>> Peter Dalgaard, Professor,
>>>> Center for Statistics, Copenhagen Business School
>>>> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
>>>> Phone: (+45)38153501
>>>> Office: A 4.23
>>>> Email: pd.mes at cbs.dk  Priv: PDalgd at gmail.com
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>> 
>>> _______________________________________________
>>> R-SIG-Mac mailing list
>>> R-SIG-Mac at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>> 
>> 
> 
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David Winsemius
Alameda, CA, USA



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