Without trigonometric substitution, integration by parts, or appeal to the geometric interpretation of the integral, we need to devise some quite fortuitous manipulations. We proceed, therefore, and write
$$\begin{align}
\sqrt{R^2-x^2}&=\frac12 \left(\sqrt{R^2-x^2}+\sqrt{R^2-x^2}\right)\\\\
&=\frac12 \left(\sqrt{R^2-x^2}+\sqrt{R^2-x^2}\right)+\frac{x^2}{\sqrt{R^2-x^2}}-\frac{x^2}{\sqrt{R^2-x^2}}\\\\
=&\frac12 \left(\sqrt{R^2-x^2}-\frac{x^2}{\sqrt{R^2-x^2}}\right)+\frac12\left(\sqrt{R^2-x^2}+\frac{x^2}{\sqrt{R^2-x^2}}\right)\\\\
&=\frac12 \frac{d\left(x\sqrt{R^2-x^2}\right)}{dx}+\frac12\left(R^2-x^2\right)\left(\frac{1}{\sqrt{R^2-x^2}}+\frac{x^2}{(R^2-x^2)^{3/2}}\right)\\\\
&=\frac12 \frac{d\left(x\sqrt{R^2-x^2}\right)}{dx}+\frac12\left(R^2-x^2\right)\frac{d\left(x/\sqrt{R^2-x^2}\right)}{dx}\\\\
&=\frac12 \frac{d\left(x\sqrt{R^2-x^2}\right)}{dx}+\frac12R^2\left(\frac{1}{1+\left(\frac{x}{\sqrt{R^2-x^2}}\right)^2}\right)\frac{d\left(x/\sqrt{R^2-x^2}\right)}{dx}\\\\
&=\frac{d}{dx}\left(\frac12 x\sqrt{R^2-x^2}+\frac12 R^2 \arctan\left(\frac{x}{\sqrt{R^2-x^2}}\right) \right)
\end{align}$$
Therefore, we arrive at
$$\begin{align}
\int_{-a}^a\sqrt{R^2-x^2}\,dx&=2\int_0^a \sqrt{R^2-x^2}\,dx\\\\
&=\left.\left( x\sqrt{R^2-x^2}+ R^2 \arctan\left(\frac{x}{\sqrt{R^2-x^2}}\right) \right)\right|_0^a\\\\
&= a\sqrt{R^2-a^2}+ R^2 \arctan\left(\frac{a}{\sqrt{R^2-a^2}}\right)
\end{align}$$