clang: error: unsupported option '-fopenmp'

[binxiangni]

When I test codes in MacOS, the error message above showed up. I tried some methods on stackoverflow but they didn't work. Any idea?

[coatless]

Read: http://thecoatlessprofessor.com/programming/openmp-in-r-on-os-x/

[binxiangni]

The initial error disappeared after I followed the instructions from the post, but a new one comes out:

checking whether we are cross compiling... configure: error: in `/private/var/folders/xn/46r52scd6_v17k8qb28tpflh0000gn/T/RtmpPQupxB/Rbuild282a768a148a/RcppArmadillo':
configure: error: cannot run C++ compiled programs.
If you meant to cross compile, use `--host'.
See `config.log' for more details

[coatless]

1. Installed Xcode CLI
2. Installed clang4 (once) with the installer? (Check only one LDFLAGS is set in ~/.R/Makevars)
3. Installed gfortran 6.1
4. Restarted R?

[binxiangni]

Now I reinstall Xcode, then the error is away. Thanks! 👍

[gurol]

Use https://github.com/coatless/r-macos-rtools

[eddelbuettel]

@gurol ? We have made half a dozen releases since that report, rewrote the architecture detection and have just seen R Core give us new macOS tools. The comment may be a little out of sync, as well-intended as it may be.

[dpastoor]

@eddelbuettel not completely out of of sync - from @vjd after fresh R OSX install + new macOS tools getting this exact error

[vjd]

@dpastoor thanks.
@eddelbuettel My MakeVars looks like this.

CC=/usr/local/clang6/bin/clang
CXX=/usr/local/clang6/bin/clang++
LDFLAGS=-L/usr/local/clang6/lib

[eddelbuettel]

@coatless Can you chime in? Which clang version should people use? What documentation should we point to? I was under the impression this was now ironed out?

[kylebaron]

No issues here:

F77 = /usr/local/bin/gfortran
FC = $F77
CXX = ccache /usr/local/clang6/bin/clang++  -Wall
LDFLAGS=-L/usr/local/clang6/lib
CC= ccache /usr/local/clang6/bin/clang
SHLIB_CXXLD=ccache /usr/local/clang6/bin/clang++
CXX11 = ccache /usr/local/clang6/bin/clang++
CXX98 = ccache /usr/local/clang6/bin/clang++
CXX14 = ccache /usr/local/clang6/bin/clang++

[coatless]

@eddelbuettel in short, I gotta spend time updating documentation for the R 3.5.* line as it uses clang6 instead of clang4...

[vjd]

@kylebmetrum My makevars reflects what you have mostly, so I don't see an issue. I updated to reflect your config. Now, I get the following error below. Is this a permissions thing?

configure: error: in `/private/var/folders/c1/ydghd7v17g16f0_nw47gvqmm0000gn/T/RtmpVeAriM/R.INSTALLab22eb1a962/RcppArmadillo':
configure: error: C++ compiler cannot create executables
See `config.log' for more details
ERROR: configuration failed for package ‘RcppArmadillo’
* removing ‘/Users/vijay/Dropbox (Personal)/rlibs/RcppArmadillo’
Warning in install.packages :
  installation of package ‘RcppArmadillo’ had non-zero exit status

[coatless]

@vjd post the config.log and your ~/.R/Makevars

[coatless]

The issue we are running into here is the binary from R is configured for usage on CRAN. Local machines still need a lot of options set.

[vjd]

@coatless I used the same ~/.R/Makevars as @kylebmetrum

where can I find the config.log?

[coatless]

Should be in /private/var/folders/c1/ydghd7v17g16f0_nw47gvqmm0000gn/T/RtmpVeAriM/R.INSTALLab22eb1a962/RcppArmadillo

[vjd]

That's where I tired initially.. but is this temp folder blown away after failed install?

[eddelbuettel]

Maybe do it the other way around: create a temp directory, change into it, copy the RcppArmadillo tarball, unpack it and run ./configure. The log file will be there. R does the same for you but cleans up temp dirs which you do not want now.

[vjd]

@eddelbuettel Thanks. I went through the config file as you suggested and realized that ccache may have been an alias in @kylebmetrum Makevars . Once I removed that and reran the installation, it worked fine.

To summarise -
I was upgrading to R 3.5 on MacOS Sierra and subsequently was updating the Rcpparmadillo package. I used the macos tools from here - https://cran.r-project.org/bin/macosx/tools/ to download clang6 and gfortran.

My initial Makevars looked like this -

CC=/usr/local/clang6/bin/clang
CXX=/usr/local/clang6/bin/clang++
LDFLAGS=-L/usr/local/clang6/lib

This caused failed installation due to the -fopenmp issue posted above.

I then updated my Makevars file to match that posted by @kylebmetrum. I had to remove the ccache which is probably an alias and my final Makevars file looks like this now.

F77 = /usr/local/bin/gfortran
FC = $F77
CXX =  /usr/local/clang6/bin/clang++  -Wall
LDFLAGS=-L/usr/local/clang6/lib
CC=  /usr/local/clang6/bin/clang
SHLIB_CXXLD=ccache /usr/local/clang6/bin/clang++
CXX11 =  /usr/local/clang6/bin/clang++
CXX98 =  /usr/local/clang6/bin/clang++
CXX14 =  /usr/local/clang6/bin/clang++

The installation was complete with this.

Thanks @coatless and @eddelbuettel

[kylebaron]

@vjd ccache is a program to speed up installation by caching; highly recommended

See: http://dirk.eddelbuettel.com/blog/2017/11/27/

And: https://ccache.samba.org/

[eddelbuettel]

Yes -- ccache is highly recommended especially when you compile the same (C/C++/...) sources multiple times -- eg when building / testing an R packages. And it is orthogonal to the what R uses. g++ and clang++ just "don't know" that they are wrapped in ccache calls.

Also, as you just relearned the hard way, do not just copy a setup blindly. You clearly could copy ccache when you did not have it installed. Sorry for the bother, it leaks out of my examples too -- but there is a wee amount of 'buyer beware' here.