[R-SIG-Mac] clang: error: unsupported option '-fopenmp'
Spencer Graves
@pencer@gr@ve@ @end|ng |rom prod@y@e@com
Tue May 7 19:20:23 CEST 2019
Adding .Renviron as you described solved the problem. Thanks. Spencer
On 2019-05-07 11:18, Balamuta, James Joseph wrote:
> 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
> >
> >
> > [[alternative HTML version deleted]]
> >
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> >
> >
>
>
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