[R-SIG-Mac] Problems with rJava fir R 3.6.1

[peter dalgaard]

I try to suppress any memories of this stuff every time I have had to deal with it, but...

Would "R CMD javareconf" help, maybe?

-pd

> On 19 Sep 2019, at 14:09 , Thomas Knox <knoxy1827 using gmail.com> wrote:
> 
> I have recently installed R 3.6.1 on my MacBook running Mac OS Mojave 10.14.5 in order to run a custom package called MH1823 (probability of detection).  This package requires me to load the following packages from CRAN, tcltk, tcltk2, survival and xlsx.
> 
> 
> 
> I have installed survival, xlsx and tlctk2 (i believe tcltk is embedded).  When I look at Package Manager i see that although the above packages are installed they are not loaded.  I can load survival but when I try to load “xlsx” i get the following  error message is:
> 
> 
> 
> Error: package or namespace load failed for ‘xlsx’:
> 
> .onLoad failed in loadNamespace() for 'rJava', details:
> 
>  call: dyn.load(file, DLLpath = DLLpath, ...)
> 
>  error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so':
> 
>  dlopen(/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so, 6): Library not loaded: /Library/Java/JavaVirtualMachines/jdk-11.0.1.jdk/Contents/Home/lib/server/libjvm.dylib
> 
>  Referenced from: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so
> 
>  Reason: image not found
> 
> starting httpd help server … done
> 
> 
> 
> 
> 
> there may be a couple of hints in here.
> 
> 
> 
> .onLoad failed in loadNamespace() for 'rJava', details  suggests the problem starts with calling rJava.
> 
> 
> 
> the next line in the error:
> 
> error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so':
> 
> I have checked this path and see no problems, everything seems to stack up and I find jJava.so where it is supposed to be.  However in the next line:
> 
> dlopen(/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so, 6): Library not loaded: /Library/Java/JavaVirtualMachines/jdk-11.0.1.jdk/Contents/Home/lib/server/libjvm.dylib
> 
> I don’t know what the number , 6 after Java.so means but have presumed version number and may be why Java8 is not working.  I also note the path …. /JavaVirtualMachines/jdk-11.0.1.jdk/ appears as . /JavaVirtualMachines/1.6.0.jdk/
> 
> suggesting a different build
> 
> 
> 
> the same occurs when I try to load the local source package MH1823
> 
> 
> 
> When I try to load HM1823 I get the error message:
> 
> * installing *source* package ‘mh1823’ ...
> 
> ** using staged installation
> 
> ** R
> 
> ** data
> 
> ** inst
> 
> ** byte-compile and prepare package for lazy loading
> 
> Error: package or namespace load failed for ‘xlsx’:
> 
> .onLoad failed in loadNamespace() for 'rJava', details:
> 
>  call: dyn.load(file, DLLpath = DLLpath, ...)
> 
>  error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so':
> 
>  dlopen(/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so, 6): Library not loaded: /Library/Java/JavaVirtualMachines/jdk-11.0.1.jdk/Contents/Home/lib/server/libjvm.dylib
> 
>  Referenced from: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so
> 
>  Reason: image not found
> 
> Error: package ‘xlsx’ could not be loaded
> 
> Execution halted
> 
> ERROR: lazy loading failed for package ‘mh1823’
> 
> * removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/mh1823’
> 
>> 
> 
> 
> 
> I find that the error message is substantially the same suggesting rJava and/or the version of Java.  I have tried removing Java 8 from my machine and installing Java 6 but don’t see any difference.  It is easy to see that Java 8 has been removed but not easy to see that 6 is installed properly as the path names are still the same.
> 
> 
> 
> When I try to load either tcltk or tcltk2, my instance of R stops responding entirely.
> 
> 
> 
> I have also installed Xquartz as I believe this is needed for Mac OS X
> 
> 
> 
> Can anyone provide some advice on what the issue might be?  I have tried reading through the FAQ’s but not found anything to point me in the right direction to correct the problem.
> 
> 
> 
> Regards,
> 
> 
> 
> Tom Knox
> 	[[alternative HTML version deleted]]
> 
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-- 
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 using cbs.dk  Priv: PDalgd using gmail.com