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A general description is here.
‘configure’ looks for support for OpenMP and if found compiles R with appropriate flags and also makes them available for use in packages: see ‘Writing R Extensions’.
This is currently experimental, and is only used in R with a single thread for ‘colSums()’ and ‘dist()’. Expect it to be more widely used in later versions of R.
This can be disabled by the ‘--disable-openmp’ flag.