[R-SIG-Mac] clang: error: unsupported option '-fopenmp'
Simon Urbanek
@|mon@urb@nek @end|ng |rom R-project@org
Wed May 15 04:48:19 CEST 2019
Just for completeness - this is in R for Mac FAQ 10.15
https://mac.r-project.org/bin/macosx/RMacOSX-FAQ.html
and in detail in R-admin 6.3.2
https://mac.r-project.org/man/R-admin.html#macOS-packages
Cheers,
Simon
> On May 7, 2019, at 13:20, Spencer Graves <spencer.graves using prodsyse.com> wrote:
>
> 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]]
>> >
>> > _______________________________________________
>> > R-SIG-Mac mailing list
>> > R-SIG-Mac using r-project.org
>> > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>> >
>> >
>>
>
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