I think we solved this via PM, I believe the short-term fix that worked was to downgrade your R version to R 3.6.0.
For others: it sounds like these dependencies have not caught up with the newest version of R/bioconductor. You can probably side step this problem by manually installing these two packages as below:
assuming OSX is your operating system:
Alternatively, these packages are not very important for the functionality of MicrobeR you might want to bypass them by downloading and editing the MicrobeR source:
Then remove the following lines from MicrobeR-Master/DESCRIPTION using your favourite text editor:
philr (>= 1.4.0),
DECIPHER (>= 2.2.0),
Then manually install from source: