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.
HTH,
-Roy
> On Nov 16, 2018, at 11:10 AM, Jonathan Greenberg <jgreenb...@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
> Gchat: jgrn...@gmail.com<mailto:jgrn...@gmail.com>, Skype: jgrn3007
>
> [[alternative HTML version deleted]]
>
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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
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
***Note new street address***
110 McAllister Way
Santa Cruz, CA 95060
Phone: (831)-420-3666
Fax: (831) 420-3980
e-mail: roy.mendelss...@noaa.gov www: http://www.pfeg.noaa.gov/
"Old age and treachery will overcome youth and skill."
"From those who have been given much, much will be expected"
"the arc of the moral universe is long, but it bends toward justice" -MLK Jr.
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