[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:
SHLIB_OPENMP_CFLAGS=
SHLIB_OPENMP_CXXFLAGS=
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!
-Dan
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
supplies?
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>>
wrote:
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
InstalledDir:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
I am still running macos Sierra ... is there a solution within this
platform? I have been getting around this by modifying Makevars when
needed
* 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
-I../inst/include/
-I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include'
-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
-I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c RcppExports.cpp -o
RcppExports.o
clang: *error: *unsupported option '-fopenmp'
make: *** [RcppExports.o] Error 1
ERROR: compilation failed for package ‘sitmo’
--
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