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

Prof Brian Ripley ripley @ending from @t@t@@ox@@c@uk
Sat Nov 17 08:13:51 CET 2018

BTW, reading the manual (in this case 'R Installation and 
Administration') often helps, and would have here.

On 16/11/2018 19:10, Jonathan Greenberg 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")'

Why are you not installing from CRAN?  Discussing off-CRAN versions here 
is frowned on, not least as we know the CRAN version works.

> 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?

That is not an *error*!  It is a warning from the OS (ld is part of the 
OS) about parts of the OS being out of step, and has been going on for 
some time (AFAIR with High Sierra too).  You have not shown us the 
complete output, but on my systems installation of CRAN rJava proceeds.

> --
> --
> 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: jgrn307 using gmail.com<mailto:jgrn307 using gmail.com>, Skype: jgrn3007

Brian D. Ripley,                  ripley using stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford

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