Understanding of nowhere dense sets The following is the definition of nowhere dense sets in Wikipedia.

In topology, a subset $A$ of a topological space $X$ is called nowhere dense (in $X$) if there is no neighborhood in $X$ on which $A$ is dense.

It is also said in this lecture note that a nowhere dense set is a set $E$ which is not dense in any ball.
I don't quite understand what "not dense in any ball" means unless I can find several essentially different counterexamples.
Considering ${\mathbb R}$ with the standard topology, I am thinking about examples which is NOT a nowhere dense set. Here are my questions:

What can be an example such that the set $E$ is dense in any ball?
What can be an example such that the set $E$ is dense in some balls while it is not in others?


I'm sure what "$E$ is dense in a ball" means. Does it mean $\overline{E}$ is a ball or $\overline{E}$ contains a ball or $\overline{E}$ is contained in a ball?
 A: Assume that $E$ and $B$ are subsets of a topological space $X$. By definition the set $E$ is dense in $B$ iff the set $E\cap B$ is dense in the subspace $B$ iff $\operatorname{cl}_B(E\cap B)=B$. Using the equality $\operatorname{cl}_B(E\cap B)=\overline{E\cap B}\cap B$ and elementary observations we obtain the equivalences
$$\operatorname{cl}_B(E\cap B)=B\ \Leftrightarrow\ \overline{E\cap B}\cap B=B\ \Leftrightarrow\ \ B\subseteq\overline{E\cap B}\cap B\ \Leftrightarrow\ B\subseteq\overline{E\cap B}\ \Leftrightarrow\ B\subseteq\bar{E}.$$
Hence $E$ is dense in $B$ iff $B\subseteq\bar{E}$.
By definition $E$ is nowhere dense in $X$ iff there is no nonempty open subset (equivalently neighborhood) of $X$ in which $E$ is dense. Using the observations above, $E$ is nowhere dense in $X$ iff $\bar{E}$ does not contain any nonempty open subset of $X$ iff $\operatorname{int}\bar{E}=\emptyset$.
Indeed, in the metric setting, $E$ is nowhere dense iff there is no ball in which $E$ is dense, since any nonempty open subset of a metric space contains a ball.
In any metric space the condition of a subset being dense in every ball is equivalent to being dense in the space, because every point of a metric space is contained in a ball. Thus any dense subset of $\mathbb{R}$, for example $\mathbb{R}$, $\mathbb{R}\setminus\{0\}$ or $\mathbb{Q}$, is an example to your first question. Regarding your second question, the ball $(-1,1)\subseteq\mathbb{R}$ is dense in itself but not dense in any ball that is not contained in $(-1,1)$.
"$E$ is dense in a ball" does not mean "$\bar{E}$ is a ball". For example $(-1,1)\cup\{2\}$ is dense in the ball $(-1,1)$ but $\bar{E}=[-1,1]\cup\{2\}$ is not a ball. However, "$\bar{E}$ is a ball" implies that "$E$ is dense in a ball": if $\bar{E}$ is a ball, then $E$ is dense in the ball $\bar{E}$.
"$E$ is dense in a ball" means "$\bar{E}$ contains a ball", since according to our observations above $E$ is dense in a set $B$ iff $B\subseteq\bar{E}$.
"$E$ is dense in a ball" does not mean "$\bar{E}$ is contained in a ball". For example $\mathbb{R}$ is dense in the ball $(-1,1)$ but no ball contains its closure. On the other hand $\bar{\emptyset}=\emptyset$ is contained in every ball but $\emptyset$ is dense in no ball.
