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
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