The behavior of BiocManager::install() for updates seems to have changed from biocLite(). Specifically, when biocLite() was executed under 'sudo R', any system R packages installed in /usr/lib/R were offered to be upgraded in /usr/local/lib/R. The new BiocManager::install() defaults to installing these in /usr/lib/R and overwriting the system copies of those packages. Is there an option that can be set that restores the prior behavior that installed any system R packages being upgraded into /usr/local/lib/R rather than overwriting the packaged copies in /usr/lib/R?