[R-SIG-Mac] clang: error: unsupported option '-fopenmp'
Balamuta, James Joseph
b@|@mut2 @end|ng |rom ||||no|@@edu
Tue May 7 18:18:55 CEST 2019
Greetings and Salutations Spencer,
Modifying the path traditionally was done in `~/.R/Makevars` by setting the implicit variables: `CXX`, `CXX11` , ...
I've found a better approach is to modify the `~/.Renviron` file. Since `.Renviron` is a "dot file", macOS will hide it by default.
You can view the .Renviron file within Finder if you enable showing dot files by using the keyboard shortcut: CMD + SHIFT + .
From terminal, the file must be created using:
touch ~/.Renviron
vi ~/.Renviron
Inside the file, add a line with:
PATH="/usr/local/clang7/bin:${PATH}"
Once done, leave `vi` by pressing the ESC key and, then, typing ":wq" in the prompt.
Regarding the gfortran uninstall, this is because there were old artifacts lying around on some users systems.
It was easier to clean the system and, then, install the toolchain relative to R.
Sincerely,
JJB
On 5/7/19, 10:24 AM, "Spencer Graves" <spencer.graves using prodsyse.com> wrote:
Hi, JJB:
Thanks. Upon reading more carefully
"https://cran.r-project.org/bin/macosx/tools/", I see that I need
clang7, not the clang8 that I previously installed. I downloaded and
installed it, but I'm confused about how to modify my path, and I'm
still getting the same error as before without that. I don't recall
ever modifying a path on a Mac before, and I don't find the
"~/.Renviron" file you mentioned.
Thanks,
Spencer Graves
p.s. I'm also a little spooked by your instructions to remove gfortran,
because it might be used by something else. I don't find
"/usr/local/gfortran" that you mention, but I do find files (not
folders) "/usr/local/bin/gfortran" and "/usr/local/bin/gfortran-4.8".
??? Thanks again.
On 2019-05-07 08:56, Balamuta, James Joseph wrote:
> Greetings and Salutations All,
>
> For R 3.6.x, you want:
>
> https://cran.r-project.org/bin/macosx/tools/clang-7.0.0.pkg
>
> To let R know about the complier, we need to modify the ~/.Renviron. You may need to create the file by running in Terminal (Applications -> Utilities):
>
> touch ~/.Renviron
>
> Then, inside of ~/.Renviron add:
>
> PATH="/usr/local/clang7/bin:${PATH}"
>
> More details can be found here (disclaimer: I wrote it):
>
> http://thecoatlessprofessor.com/programming/r-compiler-tools-for-rcpp-on-macos/
>
> I'm working on updating a bash-script installer to autodetect and install the appropriate toolchain based on the installed version of R here:
>
> https://github.com/rmacoslib/r-macos-rtools
>
> I'll update the list-serv when I've released a new version for R 3.6.x.
>
> Sincerely,
>
> JJB
>
>
>
> On 5/7/19, 8:34 AM, "R-SIG-Mac on behalf of Spencer Graves" <r-sig-mac-bounces using r-project.org on behalf of spencer.graves using prodsyse.com> wrote:
>
> Hi, Bryon et al.:
>
>
> Thanks. I did that and got virtually the same response ending
> with "clang: error: unsupported option '-fopenmp'".
>
>
> Specifically, I started by looking for a "clang" subdirectory
> under "/usr/local/", which is where clang-8.0.0.pkg from
> "https://cran.r-project.org/bin/macosx/tools/" installed. I did not
> find one. I then downloaded and installed Clang8, and it appeared in
> directory "/usr/local/clang8". I then rebooted and tried "R CMD build
> bssm" as before with the following results:
>
>
> > R CMD build bssm
> * checking for file ‘bssm/DESCRIPTION’ ... OK
> * preparing ‘bssm’:
> * checking DESCRIPTION meta-information ... OK
> * cleaning src
> * installing the package to build vignettes
> -----------------------------------
> * installing *source* package ‘bssm’ ...
> ** using staged installation
> ** libs
> clang++ -std=gnu++11
> -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
> -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include"
> -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include"
> -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include"
> -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/ramcmc/include"
> -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/sitmo/include"
> -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
> -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c R_approx.cpp -o
> R_approx.o
> clang: error: unsupported option '-fopenmp'
> make: *** [R_approx.o] Error 1
> ERROR: compilation failed for package ‘bssm’
> * removing
> ‘/private/var/folders/mh/mrm_14nx19g13lsnj9zmvwjr0000gn/T/Rtmp7TLdXk/Rinst6842b1d5fb3/bssm’
> -----------------------------------
> ERROR: package installation failed
>
>
> Suggestions?
> Thanks,
> Spencer
>
>
> On 2019-05-06 18:19, Byron Ellis wrote:
> > Hi Spencer,
> >
> > You'll want to get the compiler tools from
> > https://cran.r-project.org/bin/macosx/tools/ to build properly.
> >
> > Best,
> > B
> >
> >
> >
> > On Mon, May 6, 2019 at 4:17 PM Spencer Graves
> > <spencer.graves using prodsyse.com <mailto:spencer.graves using prodsyse.com>> wrote:
> >
> > Hello, All:
> >
> >
> > I'm getting "clang: error: unsupported option '-fopenmp'" when
> > trying to build "https://github.com/helske/bssm" under macOS 10.14.14
> > with R 3.6.0; see below.
> >
> >
> > What do you suggest?
> >
> >
> > Thanks,
> > Spencer Graves
> >
> >
> > p.s. Helske told me he thought my compiler was out of date. However,
> > I've so far been unable to find instructions that are sufficiently
> > current to convince me I might not do more harm than good
> > following them.
> >
> >
> > > R CMD build bssm
> > * checking for file ‘bssm/DESCRIPTION’ ... OK
> > * preparing ‘bssm’:
> > * checking DESCRIPTION meta-information ... OK
> > * cleaning src
> > * installing the package to build vignettes
> > -----------------------------------
> > * installing *source* package ‘bssm’ ...
> > ** using staged installation
> > ** libs
> > clang++ -std=gnu++11
> > -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
> > -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include"
> >
> > -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include"
> >
> > -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include"
> >
> > -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/ramcmc/include"
> >
> > -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/sitmo/include"
> >
> > -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
> > -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c R_approx.cpp -o
> > R_approx.o
> > clang: error: unsupported option '-fopenmp'
> > make: *** [R_approx.o] Error 1
> > ERROR: compilation failed for package ‘bssm’
> > * removing
> > ‘/private/var/folders/mh/mrm_14nx19g13lsnj9zmvwjr0000gn/T/RtmppA2gBg/Rinst24427c5cbfeb/bssm’
> > -----------------------------------
> > ERROR: package installation failed
> >
> > _______________________________________________
> > R-SIG-Mac mailing list
> > R-SIG-Mac using r-project.org <mailto:R-SIG-Mac using r-project.org>
> > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >
> >
> >
> > --
> > Byron Ellis (byron.ellis using gmail.com <mailto:byron.ellis using gmail.com>)
> > "Oook" -- The Librarian
>
>
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>
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