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I had the same error, I found a workaround by removing all highlight keywords from the \addplots and then adding a copy of one of the \addplots at the end, this time with all the highlights options and without legend. The bug appears in this MWE modified from here : \documentclass[tikz]{standalone} \usepackage{pgfplots} \pgfplotsset{compat=newest} ...


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If you just want to highlight the first occurrences without defining them explicitly and while keeping the option for plurality, etc. you can use: \usepackage{glossaries} \makeglossaries \let\oldgls\gls \let\oldGls\Gls \let\oldglspl\glspl \let\oldGlspl\Glspl \makeatletter \newcommand\term[1]{% \newglossaryentry{#1}{ name=#1, description=foo }% ...


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I am not entirely sure why the newline appears. It must be an incomparability between the todonotes and lineno packages. Your hack of using \vspace to fix this issue is probably as good as anything. One way to fix the incorrect line numbering is to "manually" decrement the counter used by the lineno package. You can write your code a little more ...



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