Trouble loading/installing rJava on Mac

[Toby Maxwell]

Hi all, it seems to be a common problem, but I can't get rJava to install or load properly, I have updated all of my R and Rstudio software, running mac OS 10.12.4, Sierra.

I used to be able to run it, but the problem started after updating R. Now when trying to load rJava I get the following errors. Not sure if anyone has any pointers, I included some of my 'steps' i.e. failures below.

Thanks!!

Toby

-Trying to load the package:

Error: package or namespace load failed for ‘rJava’:

 .onLoad failed in loadNamespace() for 'rJava', details:

  call: dyn.load(file, DLLpath = DLLpath, ...)

  error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava/libs/rJava.so':

  dlopen(/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava/libs/rJava.so, 6): Library not loaded: @rpath/libjvm.dylib

  Referenced from: /Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava/libs/rJava.so

  Reason: image not found

-A number of online help forums suggest that I need to reinstall java and tell rjava where to find it, which I did and didn't get much out of it.

done by opening R Studio via the terminal:

LD_LIBRARY_PATH=$(/usr/libexec/java_home)/jre/lib/server: open -a RStudio

-I noticed as I tried reinstalling rJava that the rJava install comes up with the following error:

clang: error: unsupported option '-fopenmp'

make[2]: *** [libjri.jnilib] Error 1

make[1]: *** [src/JRI.jar] Error 2

make: *** [jri] Error 2

ERROR: compilation failed for package ‘rJava’

* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava’

* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava’

Warning in install.packages :

  installation of package ‘rJava’ had non-zero exit status

--

Toby Maxwell

Ph.D. Candidate
Plant and Environmental Sciences Building, 3242
Department of Land, Air, and Water Resources
Agricultural and Environmental Chemistry Graduate Group

[Alex Mandel]

The error in the package install indicates that the Clang compiler isn't
working. Online others have reported that using the C++ compiler from
gcc (possibly installed via homebrew) might work better.

Poking around online led to
https://gist.github.com/hrbrmstr/6f228eead691e72bd0272a25319ea9ee which
answers
http://stackoverflow.com/questions/43632512/cannot-install-rjava-from-source-as-c-compiler-works-no?noredirect=1#comment74322210_43632512

I did also see a suggestion that installing OpenMP might solve the Clang
error, but that wasn't rJava specific.

Note for Mac/Linux users, whenever you update Java do a R CMD javareconf
before updating R packages that require Java.

Enjoy,
Alex Mandel, PhD

Center for Spatial Sciences
http://spatial.ucdavis.edu
Geospatial and Farming Systems Research Consortium
http://gfc.ucdavis.edu
University of California, Davis

[Spencer Mathews]

It's now possible to install R (and RStudio) through Anaconda. Managing your R packages using Conda should ease dependency management and circumvent these frustrating build issues.

No promises, but this could be an easy solution (rJava is available through the conda R channel).

Check out:
https://www.continuum.io/blog/developer/jupyter-and-conda-r
https://docs.continuum.io/anaconda/r_language

Good luck,

Spencer

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[Toby Maxwell]

Worked on the various forum based options with no luck.

Installed via anaconda then it was happy.

Thanks y'all.

Toby

[Matt Espe]

In my experience, most issues with R and Java can be solved with:

R CMD javareconf

At the terminal, then re-installing rJava. Might be worth a try next time before switching to a different distribution system. Anaconda is both convenient and another thing to troubleshoot when something does not work. 

Matt

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