Using OSX? Compiling an R package from source? Issues with ‘-fopenmp’? Try this.
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You can file this one under “I may have the very specific solution if you’re having exactly the same problem.”
So: if you’re running some R code and you see a warning like this:
Warning message:
In checkMatrixPackageVersion() : Package version inconsistency detected.
TMB was built with Matrix version 1.2.14
Current Matrix version is 1.2.15
Please re-install 'TMB' from source using
install.packages('TMB', type = 'source') or ask CRAN for a binary
version of 'TMB' matching CRAN's 'Matrix' package
And installation of TMB from source fails like this:
install.packages("TMB", type = "source")
clang: error: unsupported option '-fopenmp'
make: *** [external_metis.o] Error 1
ERROR: compilation failed for package ‘TMB’
And you use Homebrew – first, do this:
brew install llvm
Then create the file ~/.R/Makevars, if it does not exist and edit its contents to look like this:
C=/usr/local/opt/llvm/bin/clang CXX=/usr/local/opt/llvm/bin/clang++
Your R package should now compile without error. If it works as it did for me 🙂
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