Calling setThreadOptions() (i.e. with numThreads = "auto") should call Sys.unsetenv("RCPP_PARALLEL_NUM_THREADS"), otherwise, the following happens:

Sys.getenv("RCPP_PARALLEL_NUM_THREADS")
[1] ""
setThreadOptions(2)
Sys.getenv("RCPP_PARALLEL_NUM_THREADS")
[1] "2"
setThreadOptions()
Sys.getenv("RCPP_PARALLEL_NUM_THREADS")
[1] "2"

If the internal code always reads this variable, "auto" will not have the intended effect after reset.