Anush (imported from SE)
I am using beamer and smashoperator as follows:

\documentclass[xcolor={rgb}]{beamer}
\setbeamercovered{transparent}
\setbeamersize{text margin left=10mm,text margin right=5mm}
\setbeamertemplate{frametitle}[default][center]
\usepackage{mathtools}
\usepackage{bm}
\newcommand{\var}[1]{\operatorname{var}{#1}}
\newcommand{\E}{\mathbb{E}}
\newcommand{\norm}[1]{\left\lVert#1\right\rVert}
\begin{document}
\begin{frame}[t]
\begin{align*}
\onslide<2->{&= \E\Bigl( g(a)^2 \smashoperator{\sum_{j\in[n]\backslash\{a\}}} f^2_j Y^2_j + \smashoperator{\sum_{\substack{j\in[n]\setminus\{a\}\\i\ne j}}} f_i f_j g(i) g(j) Y_i B_j\Bigr) -{}\\}
\onslide<3->{&= \sum_{j\in[n]\backslash\{a\}} \frac{f^2_j}{k} + 0 - 0\\[\jot]}
\end{align*}
\end{frame}
\end{document}

However this gives an odd result.

[![enter image description here][1]][1]

Is there any way to fix this?

[1]: https://i.stack.imgur.com/iGhkL.png
marmot
I think you have discovered a bug, and you got already an excellent workaround. However, here is another way to obtain this result, which might be even a bit shorter. More importantly, the fact that this method works may allow us to come up with educated guesses on what's going on. All you need to do is to ["repair" the \pause command](https://topanswers.xyz/tex?q=1126#a1350). I do not want to repeat all information from the linked post, but the align and so on environments "run" the code twice, one time in a "measuring" phase and then "for real". By suppressing the measuring phase in \pause, your issue gets solved, too. This seems to suggest that the \smashoperator uses the "wrong" boxes in the subscripts of the sum.


\documentclass[xcolor={rgb}]{beamer}
\setbeamercovered{transparent}
\setbeamersize{text margin left=10mm,text margin right=5mm}
\setbeamertemplate{frametitle}[default][center]
\usepackage{mathtools}
\usepackage{bm}
\newcommand{\var}[1]{\operatorname{var}{#1}}
\newcommand{\E}{\mathbb{E}}
\newcommand{\norm}[1]{\left\lVert#1\right\rVert}
\makeatletter
\renewrobustcmd{\beamer@@pause}[1][]{%
\unless\ifmeasuring@%
\ifblank{#1}%
{\stepcounter{beamerpauses}}%
{\setcounter{beamerpauses}{#1}}%
\onslide<\value{beamerpauses}->\relax%
\fi
}
\makeatother
\begin{document}
\begin{frame}[t]
\pause
\begin{align*}
&= \E\Bigl( g(a)^2 \smashoperator{\sum_{j\in[n]\backslash\{a\}}} f^2_j Y^2_j + \smashoperator{\sum_{\substack{j\in[n]\setminus\{a\}\\i\ne j}}} f_i f_j g(i) g(j) Y_i B_j\Bigr) -{}\\
\pause
&= \sum_{j\in[n]\backslash\{a\}} \frac{f^2_j}{k} + 0 - 0\\[\jot]
\end{align*}
\end{frame}
\end{document}

![ani.gif](/image?hash=99ceb90a047f4c8077f34fb08a0323cf2ecd69272353fb6e5ff4ac516ccbb5f5)
samcarter
As a workaround, you can add the colour yourself:


\documentclass[xcolor={rgb}]{beamer}
\setbeamercovered{transparent}
\setbeamersize{text margin left=10mm,text margin right=5mm}
\setbeamertemplate{frametitle}[default][center]
\usepackage{mathtools}
\usepackage{bm}
\newcommand{\var}[1]{\operatorname{var}{#1}}
\newcommand{\E}{\mathbb{E}}
\newcommand{\norm}[1]{\left\lVert#1\right\rVert}
\begin{document}
\begin{frame}[t]
\begin{align*}
\onslide<1->{&= \E\Bigl( g(a)^2 \smashoperator{\sum_{j\in[n]\backslash\{a\}}} f^2_j Y^2_j + \smashoperator{\sum_{\substack{j\in[n]\setminus\{a\}\\i\ne j}}} f_i f_j g(i) g(j) Y_i B_j\Bigr) -{}\\}
\onslide<3->{&= \sum_{j\in[n]\backslash\{a\}} \frac{f^2_j}{k} + 0 - 0\\[\jot]}
\end{align*}
\end{frame}
\end{document}


![document.gif](/image?hash=7b81963306e1ce7f1566d927d33018d6c9342180252ac7d754fe0ab65455e443)

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