With the usual apologies if this is a red herring: the lme4 package is getting

Found non-API call to R: ‘SET_TYPEOF’. Compiled code should not call non-API entry points in R.

NOTEs with r-devel. My best guess is that these are coming upstream from Rcpp, e.g. see here; I don't find any instances of SET_TYPEOF in the lme4, Matrix, or RcppEigen code ...