A tricky one...... I must admit to not having come across this problem before, but then I rarely use Windows for development work and host my MySQL server on Linux.
However, I have managed to track down some leads on this.
It looks like there could either be a compilation problem, or a setting in the my.cnf file might be incorrect.
Some details about the exact same error, and details about commenting out custom configuration in my.cnf file:
https://support.plesk.com/hc/en-us/articles/213940125-Error-executing-Plesk-utilities-Can-t-initialize-character-set-unknown-path-compiled-in-
Stackoverflow page discussing a similar error:
https://stackoverflow.com/questions/38813689/cant-initialize-character-set-utf8mb4-with-windows-mysql-python
MySQL Manual Page discussing a similar error. Looks like this solution might require re-compiling MySQL:
https://dev.mysql.com/doc/refman/5.7/en/cannot-initialize-character-set.html
I hope some of those links provide some clues and you can resolve this. If not, perhaps we can look at a different R library to connect to MySQL.
There's the RMariaDB package:
https://github.com/r-dbi/RMariaDB
Or you could try dplyr/dbplyr combination:
http://db.rstudio.com/dplyr