I have a project with a connection that was working properly on the same device. I suddenly got the error below. And I could connect from the same device through MySQL workbench
My code started having this exact problem after doing a system wide package update on 3/29/2017 for the first time since 2/1/2017.
Looking at the versioning for RMySQL, RMySQL_0.10.9.tar.gz published 2016-05-08 15:39 RMySQL_0.10.10.tar.gz published 2017-03-21 07:50
I reverted my version to 0.10.9 and the problem went away:
require(devtools)
install_version("RMySQL", version = "0.10.9", repos = "http://cran.us.r-project.org")
I posted your issue to the RMySQL bug page, so we'll see if they address it