[R] Problem loading packages in R 3.6.1

[David Winsemius]

On 9/19/19 1:11 AM, Jeff Newmiller wrote:
> 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.

Which down below we see requires that the java development kit be 
installed correctly for xlsx. This has been a recurrent issue on the Mac 
and there are many question about it on the correct mailing list, which 
is not rhelp, but rather R-SIG-mac.


Here's a link to the MarkLogic archive of r-sig-mac


https://markmail.org/search/?q=+list%3Aorg.r-project.r-sig-mac+install+java#query:list%3Aorg.r-project.r-sig-mac%20install%20java%20order%3Adate-backward+page:1+state:facets


... and if you don't want to use it then try rseek.org with a search 
strategy of "install java mac". If that doesn't satisfy, then subscribe 
and post a question on r-sig-mac with a full description of  results of 
trying to install a newer version of java. I have version 10.0.1 on my 
Mojave laptop.


-- 

David.

>> 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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