Bookdown – theorem references within math?

I am using Bookdown, and I would like to refer to a theorem in the middle of a mathematical derivation. The closest I have got is to use

\begin{align*} b^2 &= c^2 -a^2  \text{ by Theorem @ref(thm:pythagoras)} \\ \end{align*} 

where I have previously defined a theorem labelled pythagoras as follows

```{theorem, label="pythagoras"} $c^2=a^2+b^2$ ``` 

The pdf output renders as I would like, but the HTML does not.

Looking at the HTML source, the problem is that MathJAX has broken due to the inclusion of a link of the form <a href=""></a>. It works if I manually remove the hyperlink, however this is not a practical solution as I have quite a lot of these in my document.

Is there a way to fix this?

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