[R-SIG-Mac] rJava stops loading since I upgraded R to 3.4.0
Christofer Bogaso
bogaso.christofer at gmail.com
Wed May 24 16:40:05 CEST 2017
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
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
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>
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>
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