[Bioc-devel] -fopenmp switch issue on mac

Bunis, Daniel D@n|e|@Bun|@ @end|ng |rom uc@|@edu
Wed Dec 4 21:10:05 CET 2019

I was running into the `clang: *error: *unsupported option '-fopenmp’` yesterday myself.  I’m not on Sierra, but I fixed it with the top answer on this page: https://stackoverflow.com/questions/43595457/alternate-compiler-for-installing-r-packages-clang-error-unsupported-option/43943631#43943631?newreg=e3bd1c44b597485f981795398d9432b6.

Specifically, I used the solution #3 there to turn of the addition of the -fopenmp option:
1) Made a folder in my `~/` called .R
2) Made a file in ~/.R/Makevars containing:


Then I was able to install all the packages for which I’d been getting the -fopenmp error.

I hope this solution works for you as well!

On Dec 4, 2019, at 8:07 AM, Kasper Daniel Hansen <kasperdanielhansen using gmail.com<mailto:kasperdanielhansen using gmail.com>> wrote:

Are you using the clang 6 (R 3.5) / 7 (R 3.6) / 8 (R 4.0) which Simon

This is for clang 6 with full path

/usr/local/clang6/bin/clang --version
clang version 6.0.0 (tags/RELEASE_600/final)
Target: x86_64-apple-darwin18.7.0
Thread model: posix
InstalledDir: /usr/local/clang6/bin

On Wed, Dec 4, 2019 at 11:03 AM Vincent Carey <stvjc using channing.harvard.edu<mailto:stvjc using channing.harvard.edu>>

When installing packages from source,

I frequently run into this error with

%vjcair> clang --version

Apple LLVM version 9.0.0 (clang-900.0.39.2)

Target: x86_64-apple-darwin16.7.0

Thread model: posix



I am still running macos Sierra ... is there a solution within this
platform?  I have been getting around this by modifying Makevars when

* installing *source* package ‘sitmo’ ...

** package ‘sitmo’ successfully unpacked and MD5 sums checked

** using staged installation

** libs

clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG

-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
-I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c RcppExports.cpp -o

clang: *error: *unsupported option '-fopenmp'

make: *** [RcppExports.o] Error 1

ERROR: compilation failed for package ‘sitmo’

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