[Bioc-devel] -fopenmp switch issue on mac

[Vincent Carey]

Thanks -- the solution I used was to install the Simon-Urbanek-modified
distribution clang 8.0 from the page noted in my reply.

On Wed, Dec 4, 2019 at 3:10 PM Bunis, Daniel <Daniel.Bunis using ucsf.edu> wrote:

> 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> 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>
> 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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>
>
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