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

[Jonathan Greenberg]

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 <ripley using stats.ox.ac.uk<mailto:ripley using 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>"), 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
> http://www.unr.edu/nres
> Gchat: jgrn307 using gmail.com<mailto:jgrn307 using gmail.com><mailto:jgrn307 using gmail.com<mailto:jgrn307 using gmail.com>>, Skype: jgrn3007


--
Brian D. Ripley,                  ripley using stats.ox.ac.uk<mailto:ripley using stats.ox.ac.uk>
Emeritus Professor of Applied Statistics, University of Oxford

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--
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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

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