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 <knoxy1...@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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______________________________________________
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
