Using OSX? Compiling an R package from source? Issues with ‘ -fopenmp ’ ? Try this.

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 :)
Source: What You're Doing Is Rather Desperate - Category: Bioinformatics Authors: Tags: programming statistics compiler llvm osx Source Type: blogs