In an effort to pin it down, outside of Rcmdr or any
packages other than tcltk itself, I came up with a simple
reproducible example. Essentially, the sequence that gives
the warnings is
tktoplevel()
[then close the Tk window using the window controls]
X11()
tktoplevel()
[then close the Tk window using the wondow controls]
Closing the second Tk window is the act that seems to
provoke the warnings (see the two session transcripts
below). The number of warnings is different on my two
systems, but I don't know whather that's to do with OS, or
X11, or the two different versions of R, or what.
Without the call to X11(), I do not get the warnings. And
the call to X11() seemingly needs to come *after* the first
tktoplevel() call in order for the warnings to be
generated.
Unfortunately I do not have access to other systems on which
to test this, or the necessary knowledge of X11, Tk etc to
be able to debug it. I am noting it here only in the hope
that it might be useful to someone else on R-devel who is
better placed to identify the likely cause(s).