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

Wed May 24 23:42:24 CEST 2017

After performing all your instructions, I am now be able to load
rJava. Thanks all for your support. Regards,

On Wed, May 24, 2017 at 8:51 PM, Brandon Hurr <brandon.hurr at gmail.com> wrote:
> xcode-select --install
>
> And see if you have the command line tools installed.
>
> Brandon
>
> On Wed, May 24, 2017 at 8:19 AM, David Winsemius <dwinsemius at comcast.net>
> wrote:
>>
>>
>> > 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
>> >>>
>> >>
>> >
>> > _______________________________________________
>> > R-SIG-Mac mailing list
>> > R-SIG-Mac at r-project.org
>> > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>
>> David Winsemius
>> Alameda, CA, USA
>>
>> _______________________________________________
>> R-SIG-Mac mailing list
>> R-SIG-Mac at r-project.org
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>
>