[R] Problem loading packages in R 3.6.1

[Jeff Newmiller]

Since no answer has been forthcoming, my advice is to read the Posting Guide. There is a more appropriate list for your question, and you should take the warning about posting using plain text format on all r-project mailing lists seriously.

On September 17, 2019 9:55:31 AM PDT, 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.
>
>Regards,
>
>Tom Knox
>	[[alternative HTML version deleted]]
>
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-- 
Sent from my phone. Please excuse my brevity.