From http://opiateforthemass.es/articles/why-i-dont-like-jupyter-fka-ipython-notebook/

This is maybe R specific, but I made an experience that the output is incomplete. Especially if you work with ggplot. Some warning messages don’t appear in the notebook, but in the terminal, you started the notebook from. This is annoying, because actually that means that you should check your terminal and your output after every command you run to make sure not to miss warnings and error messages.

@Quiri: could you post a small example where this happens?