\pgfplots@stacked@diff undefined
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#219 \pgfplots@stacked@diff undefined
This is related to https://sourceforge.net/p/pgf/bugs/512/ but it's not clear whether this is a PGF or pgfplots bug. It definitely surfaced after the PGF 3.1 update. However, it can be easily fixed by just defining \pgfplots@stacked@diff.
% used PGFPlots v1.16
\documentclass[border=5pt]{standalone}
\usepackage{pgfplots}
\pgfplotsset{compat=1.16}
\makeatletter
% \def\pgfplots@stacked@diff{}
\makeatother
\usepackage{filecontents}
\begin{filecontents*}{123.tsv}
x y
0.9 NaN
1 0.1
1.2 0.2
\end{filecontents*}
\begin{document}
\begin{tikzpicture}
\begin{axis}[
unbounded coords=jump,
stack plots=y,
]
\addplot table {123.tsv};
\addplot table {123.tsv};
\end{axis}
\end{tikzpicture}
\end{document}
Discussion
I have modified the above MWE a bit to exclude stuff that is not relevant.
I can confirm that this bug occurs (only), when the first coordinate is
NaN(or filtered away).