Ok, figured it out but it was non-trivial. I found the solution here: https://github.com/velocyto-team/velocyto.R/issues/2#issuecomment-352584213
TLDR you need to use homebrew (https://brew.sh/): 1) Install homebrew as linked above 2) Install llvm (and maybe boost): brew install llvm brew install boost 3) Mod your ~/.R/Makevars (nano ~/.R/Makevars) to read: CC=/usr/local/clang4/bin/clang CXX=/usr/local/clang4/bin/clang++ CXX11=/usr/local/clang4/bin/clang++ CXX14=/usr/local/clang4/bin/clang++ CXX17=/usr/local/clang4/bin/clang++ CXX1X=/usr/local/clang4/bin/clang++ LDFLAGS=-L/usr/local/clang4/lib That allowed me to properly get rj and rj.gd<http://rj.gd> working again which then allowed me to start using Stat-ET again. I imagine this will solve other problems MacOS X Mojave package installs. --jonathan On Sat, Nov 17, 2018 at 5:50 AM Jonathan Greenberg <jgreenb...@unr.edu<mailto:jgreenb...@unr.edu>> wrote: I'm aware rJava can be installed as a binary and that this is an OS issue, hence posting on r-sig-mac. I assumed more people are familiar with rJava then rj and I'm fairly confident it's the same issue, hence my showing that error. rj is not on CRAN AFAIK so I'm trying to solve the source install issue for that particular package. The manual and the website have not, this far, led me to getting this working. The clang and gfortran installers do not solve the issue. I suspect there is a Makevars solution but, again, I haven't found one that works. This happened post Mojave (I had everything working in High Sierra). J On Fri, Nov 16, 2018, 11:14 PM Prof Brian Ripley <rip...@stats.ox.ac.uk<mailto:rip...@stats.ox.ac.uk><mailto:rip...@stats.ox.ac.uk<mailto:rip...@stats.ox.ac.uk>>> wrote: 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><http://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 & > E<https://maps.google.com/?q=ural+Resources+%26+E&entry=gmail&source=g>nvironmental > Science > University of Nevada, Reno > 1664 N Virginia St MS/0186 > Reno, NV 89557 > Phone: 415-763-5476<tel:(415)%20763-5476> > http://www.unr.edu/nres > Gchat: > jgrn...@gmail.com<mailto:jgrn...@gmail.com><mailto:jgrn...@gmail.com<mailto:jgrn...@gmail.com>><mailto:jgrn...@gmail.com<mailto:jgrn...@gmail.com><mailto:jgrn...@gmail.com<mailto:jgrn...@gmail.com>>>, > Skype: jgrn3007 -- Brian D. Ripley, rip...@stats.ox.ac.uk<mailto:rip...@stats.ox.ac.uk><mailto:rip...@stats.ox.ac.uk<mailto:rip...@stats.ox.ac.uk>> Emeritus Professor of Applied Statistics, University of Oxford _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org<mailto:R-SIG-Mac@r-project.org><mailto:R-SIG-Mac@r-project.org<mailto:R-SIG-Mac@r-project.org>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac -- -- 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<tel:(415)%20763-5476> http://www.unr.edu/nres Gchat: jgrn...@gmail.com<mailto:jgrn...@gmail.com><mailto:jgrn...@gmail.com<mailto:jgrn...@gmail.com>>, Skype: jgrn3007 [[alternative HTML version deleted]] _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org<mailto:R-SIG-Mac@r-project.org> https://stat.ethz.ch/mailman/listinfo/r-sig-mac -- -- 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]] _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
