This will be a very short post. It addresses a problem I had and I have seen others ask about on various forums (but with no answer).

The problem

The icons have disappeared from the top of some of my R chunks in my R Markdown document.

Notice how there is no settings icon, or the little green run icon in the second R chunk. If you have eagle eyes you will see why.

The solution

If you look very closely in Figure 1, you will see there is an extra set of back ticks at the end of the chunk. Remove these and you fix the problem.

This might seem blindingly obvious to some, but it is really easy to miss in a large Markdown document. It also has follow on consequences in that it makes it harder to run lines of code in a chunk—you have to select them before using Cmd/Ctrl-Enter.

But wait! There’s more!

This just in, highlighted by Twitter pal Michael MacAskill (@Sakkaden). A space between the ``` and the {r} can cause the same problem.

Thanks Michael!