When you execute code in a notebook, an indicator will appear in the gutter to show you execution progress. Lines of code which have been sent to R are marked with dark green; lines which have not yet been sent to R are marked with light green.
Running or Re-Running individual chunks by pressing Run for all the chunks present in a document can be painful. We can use Run All from the Insert menu in the toolbar to Run all the chunks present in the notebook. Keyboard shortcut is Ctrl + Alt + R (OS X: Cmd + Option + R)
There’s also a option Restart R and Run All Chunks command (available in the Run menu on the editor toolbar), which gives you a fresh R session prior to running all the chunks.