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rJava stops loading since I upgraded R to 3.4.0

14 messages · Duncan Murdoch, Christofer Bogaso, Peter Dalgaard +3 more

Original
Christofer Bogaso
# 
Hi again,

After I upgraded R to 3.4.0, I could not load rJava package. Below is
the error :
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

I have installed latest version of Java.

R version :

R version 3.4.0 (2017-04-21) -- "You Stupid Darkness"

Copyright (C) 2017 The R Foundation for Statistical Computing

Platform: x86_64-apple-darwin15.6.0 (64-bit)

iOS : Sierra

With previous version of R, rJava was working fine. Could you please
help how to fix it.

Thanks for your time.

Regards,
Duncan Murdoch
#
On 23/05/2017 2:48 PM, Christofer Bogaso wrote:
Did you re-install rJava?  Generally speaking you need to re-install all 
packages when switching R versions (except if the only change is in the 
patch level z, where the version number is x.y.z, you can usually use 
the old version).

Duncan Murdoch
Christofer Bogaso
# 
Hi Duncan, yes I reinstalled again the rJava, but the problem persists.

On Wed, May 24, 2017 at 1:35 AM, Duncan Murdoch
<murdoch.duncan at gmail.com> wrote:
David Winsemius
# 
To Christofer;

Does '/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava/libs/rJava.so' exist?

(You may need to check libPaths() in your new installation. )
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.

Good luck;
David,
David Winsemius
Alameda, CA, USA
Peter Dalgaard
# 
[Christofer seemed to have fallen off the cc: list, now included]
I am, and rJava doesn't load here either. However after

sudo R CMD javareconf

it seems happy as a clam.

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Christofer Bogaso
    

    

      
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Hi David,

The file 'rJava.so' exists in my machine :

            

      
      
      
    

        
[1] TRUE

Also the Javac version that I have :

            

      
      
      
    

        
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.

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:

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      David Winsemius
    

    

      
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You might also want to report the value that Sys.getenv() returns for:

DYLD_LIBRARY_PATH  

For me it is now:

       /Library/Java/JavaVirtualMachines/jdk1.8.0_131.jdk/Contents/

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

        
David Winsemius
Alameda, CA, USA

  
  


  


      

    

    

      
      

        


  

        

      David Winsemius
    

    

      
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Yes, it does and some people seem to get success with that. I found that installing 1.8 (also confusingly known as "Java 8") resolved my difficulties with loading rJava. I'm not an expert, just reporting my ezxperience

            

      
      
      
    

        
For my machine:

            

      
      
      
    

        
DYLD_LIBRARY_PATH        /Library/Java/JavaVirtualMachines/jdk1.8.0_131.jdk/Contents/

            

      
      
      
    

        
David Winsemius
Alameda, CA, USA

  
  


  


      

    

    

      
      

        


  

        

      David Winsemius
    

    

      
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And I just notice another value in the returns from that command:

LD_LIBRARY_PATH           :@JAVA_LD@

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Simon Urbanek
    

    

      
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Christofer,

            

      
      
      
    

        
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

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Christofer Bogaso
    

    

      
      #
    

  


  

      
Hi,

I have installed javac to it's latest version, still the problem
persists. Below is the latest result

            

      
      
      
    

        
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

            

      
      
      
    

        
[1] TRUE

            

      
      
      
    

        
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:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      David Winsemius
    

    

      
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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.

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Brandon Hurr
    

    

      
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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:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Christofer Bogaso
    

    

      
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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: