Please see the problem description on StackOverflow. I am moving it here in RStudio Community support as I think this is RStudio IDE problem.
Unfortunately, it's hard to say for sure, but it's possible that the R code RStudio is running behind the scenes is generating warnings, and those warnings are getting plastered into the R session after control returns to the top.
It'd be helpful to see the actual warning messages, so we could have some hints as to what's going on.
Note that RStudio runs, for example,
str() on variables in the global environment in order to populate the Environment pane, so it is possible some warnings are leaking out because of that.