Re: [R-SIG-Mac] 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"),
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: jgrn...@gmail.com, Skype: jgrn3007
--
Brian D. Ripley, rip...@stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford
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Re: [R-SIG-Mac] Issues with rj (requirement for StatET) since Mojave/3.5.1 update
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 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"),
> 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, Skype: jgrn3007
>
> [[alternative HTML version deleted]]
>
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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/
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[R-SIG-Mac] Issues with rj (requirement for StatET) since Mojave/3.5.1 update
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"),
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, Skype: jgrn3007
[[alternative HTML version deleted]]
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