There has been a little bit of discussion before of warnings carrying over in unexpected ways, sometimes possibly linked to the fact that RStudio is calling some bits of R code behind the scenes. See:
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.
Intermittently, when I execute code in rstudio server (non-pro) I get the following included with calls in R notebooks:
In scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
EOF within quoted string
I also see Error creating notebook: non-numeric argument to binary operator. See line 64. when saving. I’m not sure these are related. I’ve noticed the problems on both Firefox and Chrome, so I don’t think it’s a browser specific issue.
Is there some file somewhere I might try deleting to make these issues go away?
The first few lines of my sessionInfo are:
R version 3.4.3 (2017-11-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7…
Similar Github issue:
And I could swear I read a more involved discussion of this here or on the Github issue tracker, including an attempted fix, but I can't find it now (and maybe I imagined it!). As usual, if you can confirm that this happens only in RStudio and not in R, and find a way to reproduce the out-of-place (or just confusingly placed) warnings, that would be helpful!