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<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?
--
--
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
Issues with rj (requirement for StatET) since Mojave/3.5.1 update
9 messages · Roy Mendelssohn - NOAA Federal, Brian Ripley, Jonathan Greenberg +2 more
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 <jgreenberg at unr.edu> 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<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?
--
--
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
[[alternative HTML version deleted]]
_______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
********************** "The contents of this message do not reflect any position of the U.S. 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.Mendelssohn at noaa.gov www: http://www.pfeg.noaa.gov/ "Old age and treachery will overcome youth and skill." "From those who have been given much, much will be expected" "the arc of the moral universe is long, but it bends toward justice" -MLK Jr.
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
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 at stats.ox.ac.uk<mailto:ripley at 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 at gmail.com<mailto:jgrn307 at gmail.com><mailto:jgrn307 at gmail.com<mailto:jgrn307 at gmail.com>>, Skype: jgrn3007
-- Brian D. Ripley, ripley at stats.ox.ac.uk<mailto:ripley at stats.ox.ac.uk> Emeritus Professor of Applied Statistics, University of Oxford _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at r-project.org<mailto:R-SIG-Mac at 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: jgrn307 at gmail.com<mailto:jgrn307 at gmail.com>, Skype: jgrn3007
8 days later
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 <jgreenberg at unr.edu<mailto:jgreenberg at 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 <ripley at stats.ox.ac.uk<mailto:ripley at stats.ox.ac.uk><mailto:ripley at stats.ox.ac.uk<mailto:ripley at 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: jgrn307 at gmail.com<mailto:jgrn307 at gmail.com><mailto:jgrn307 at gmail.com<mailto:jgrn307 at gmail.com>><mailto:jgrn307 at gmail.com<mailto:jgrn307 at gmail.com><mailto:jgrn307 at gmail.com<mailto:jgrn307 at gmail.com>>>, Skype: jgrn3007
-- Brian D. Ripley, ripley at stats.ox.ac.uk<mailto:ripley at stats.ox.ac.uk><mailto:ripley at stats.ox.ac.uk<mailto:ripley at stats.ox.ac.uk>> Emeritus Professor of Applied Statistics, University of Oxford _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at r-project.org<mailto:R-SIG-Mac at r-project.org><mailto:R-SIG-Mac at r-project.org<mailto:R-SIG-Mac at 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: jgrn307 at gmail.com<mailto:jgrn307 at gmail.com><mailto:jgrn307 at gmail.com<mailto:jgrn307 at gmail.com>>, Skype: jgrn3007 _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at r-project.org<mailto:R-SIG-Mac at 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: jgrn307 at gmail.com<mailto:jgrn307 at gmail.com>, Skype: jgrn3007
On Sun, Nov 25, 2018 at 9:48 PM Jonathan Greenberg <jgreenberg at unr.edu> wrote:
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
I've recently installed llvm via homebrew, after an upgrade to Mojave. However my newly installed clang version is surely not 4 but 7, and it is not found under /usr/local/. Instead, I've edited the Makevars file with something like: CC=/usr/local/Cellar/llvm/7.0.0/bin/clang CXX=/usr/local/Cellar/llvm/7.0.0/bin/clang++ CXX1X=/usr/local/Cellar/llvm/7.0.0/bin/clang++ LDFLAGS=-L/usr/local/Cellar/llvm/7.0.0/lib -Wl,-rpath,/usr/local/Cellar/llvm/7.0.0/lib CXXFLAGS=-I/usr/local/Cellar/llvm/7.0.0/lib/clang/7.0.0/include/ This seems to work for me, Adrian -- Adrian Dusa University of Bucharest Romanian Social Data Archive Soseaua Panduri nr. 90-92 050663 Bucharest sector 5 Romania https://adriandusa.eu
On Sun, Nov 25, 2018 at 9:48 PM Jonathan Greenberg <jgreenberg at unr.edu> wrote:
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
I've recently installed llvm via homebrew, after an upgrade to Mojave. However my newly installed clang version is surely not 4 but 7, and it is not found under /usr/local/. Instead, I've edited the Makevars file with something like: CC=/usr/local/Cellar/llvm/7.0.0/bin/clang CXX=/usr/local/Cellar/llvm/7.0.0/bin/clang++ CXX1X=/usr/local/Cellar/llvm/7.0.0/bin/clang++ LDFLAGS=-L/usr/local/Cellar/llvm/7.0.0/lib -Wl,-rpath,/usr/local/Cellar/llvm/7.0.0/lib CXXFLAGS=-I/usr/local/Cellar/llvm/7.0.0/lib/clang/7.0.0/include/ This seems to work for me, Adrian -- Adrian Dusa University of Bucharest Romanian Social Data Archive Soseaua Panduri nr. 90-92 050663 Bucharest sector 5 Romania https://adriandusa.eu
3 days later
For posterity: both recommendations are plain wrong so don't use (obviously, the settings didn't match the installed compilers). They are not supported in the CRAN version of R which is compiled by the clang 6.0 compiler in /usr/local/clang6 that we supply on CRAN. You can compile your own R or use homebrew, but don't expect CRAN packages to work with that. You don't even need to touch Makevars, just setting PATH to start with /usr/local/clang6/bin before compilation is sufficient. Cheers, Simon
On Nov 26, 2018, at 1:41 AM, Adrian Du?a <dusa.adrian at gmail.com> wrote: On Sun, Nov 25, 2018 at 9:48 PM Jonathan Greenberg <jgreenberg at unr.edu> wrote:
Ok, figured it out but it was non-trivial. I found the solution here:
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
I've recently installed llvm via homebrew, after an upgrade to Mojave. However my newly installed clang version is surely not 4 but 7, and it is not found under /usr/local/. Instead, I've edited the Makevars file with something like: CC=/usr/local/Cellar/llvm/7.0.0/bin/clang CXX=/usr/local/Cellar/llvm/7.0.0/bin/clang++ CXX1X=/usr/local/Cellar/llvm/7.0.0/bin/clang++ LDFLAGS=-L/usr/local/Cellar/llvm/7.0.0/lib -Wl,-rpath,/usr/local/Cellar/llvm/7.0.0/lib CXXFLAGS=-I/usr/local/Cellar/llvm/7.0.0/lib/clang/7.0.0/include/ This seems to work for me, Adrian -- Adrian Dusa University of Bucharest Romanian Social Data Archive Soseaua Panduri nr. 90-92 050663 Bucharest sector 5 Romania https://adriandusa.eu [[alternative HTML version deleted]]
_______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
On Thu, Nov 29, 2018 at 4:06 PM Simon Urbanek <simon.urbanek at r-project.org> wrote:
For posterity: both recommendations are plain wrong so don't use
(obviously, the settings didn't match the installed compilers). They are not supported in the CRAN version of R which is compiled by the clang 6.0 compiler in /usr/local/clang6 that we supply on CRAN. You can compile your own R or use homebrew, but don't expect CRAN packages to work with that. You don't even need to touch Makevars, just setting PATH to start with /usr/local/clang6/bin before compilation is sufficient. Thanks very much Simon, will follow your instructions to be CRAN compliant. Best, Adrian