Issues with rj (requirement for StatET) since Mojave/3.5.1 update
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 at gmail.com<mailto:jgrn307 at gmail.com>, Skype: jgrn3007
Brian D. Ripley, ripley at stats.ox.ac.uk Emeritus Professor of Applied Statistics, University of Oxford