[R-SIG-Mac] Issues with rj (requirement for StatET) since Mojave/3.5.1 update

Roy Mendelssohn - NOAA Federal roy@mendel@@ohn @ending from no@@@gov
Fri Nov 16 20:32:55 CET 2018

Check that you have the latest version of the clang compiler from the r-mac site.  I believe the present version supports -fopenmp, previous version did not.  If not,  I can point you to a different link to download the compiler, but I think using the officially approved versions the cleanest solution.



> On Nov 16, 2018, at 11:10 AM, Jonathan Greenberg <jgreenberg using unr.edu> wrote:
> I'm hoping to get some insight into seeing if I can get "rj" working again in Mojave/R 3.5.1 -- this is a requirements for the Eclipse interface to R "Stat-ET") -- I'm seeing similar issues when trying to get rJava working also from source, e.g.:
> Rscript -e 'install.packages("rJava", repos="http://rforge.net", type="source")'
> and
> install.packages(c("rj", "rj.gd<http://rj.gd>"), repos="http://download.walware.de/rj-2.1",type="source")
> All issues lead to:
> "clang: error: unsupported option '-fopenmp'"
> I've installed clang6 and gfortran61 from CRAN, but that doesn't seem to work.  I've tried tweaking the ~/.R/Makevars, e.g.:
> FLIBS=-L/usr/local/gfortran/lib -lgfortran -lquadmath -lm
> CC=/usr/local/clang6/bin/clang
> CXX=/usr/local/clang6/bin/clang++
> CXX1X=/usr/local/clang6/bin/clang++
> CXX98=/usr/local/clang6/bin/clang++
> CXX11=/usr/local/clang6/bin/clang++
> CXX14=/usr/local/clang6/bin/clang++
> CXX17=/usr/local/clang6/bin/clang++
> LDFLAGS=-L/usr/local/clang6/lib
> Which only results in a different error:
> ld: warning: text-based stub file /System/Library/Frameworks//JavaVM.framework/JavaVM.tbd and library file /System/Library/Frameworks//JavaVM.framework/JavaVM are out of sync. Falling back to library file for linking.
> ld: library not found for -lomp
> Any ideas?
> --
> --
> Jonathan A. Greenberg, PhD
> Randall Endowed Professor and Associate Professor of Remote Sensing
> Global Environmental Analysis and Remote Sensing (GEARS) Laboratory
> Natural Resources & Environmental Science
> University of Nevada, Reno
> 1664 N Virginia St MS/0186
> Reno, NV 89557
> Phone: 415-763-5476
> http://www.unr.edu/nres
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"The contents of this message do not reflect any position of the U.S. Government or NOAA."
Roy Mendelssohn
Supervisory Operations Research Analyst
Environmental Research Division
Southwest Fisheries Science Center
***Note new street address***
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Santa Cruz, CA 95060
Phone: (831)-420-3666
Fax: (831) 420-3980
e-mail: Roy.Mendelssohn using noaa.gov www: http://www.pfeg.noaa.gov/

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