Warning message with fonts: Label(s) may have changed. Rerun to get cross-references right

Question

Why do XeLaTeX return this warning message:

Label(s) may have changed. Rerun to get cross-references right.

when using some fonts as Amiri and how one can get out of this warning message. I need to fix this to run arara on my files.

\documentclass[a4paper]{book}
\usepackage{fontspec} 
\usepackage[quiet,nolocalmarks]{polyglossia}  
\setmainlanguage[numerals=maghrib]{arabic}
\setotherlanguage{english}
\setmainfont[Script=Arabic]{Amiri}         % with 'Times New Roman' one get no warning
\begin{document}
\chapter{الفصل الأول}
\chapter{الفصل الثاني}
\end{document}

what are your arara instructions, you haven't put them in your mwe. — ArTourter, Dec 31 '15 at 12:46
the warning is normal, and usually goes if you do what it says and re-run latex. Do you mean that you get the warning even if you run xelatex multiple times? — David Carlisle, Dec 31 '15 at 12:54
@DavidCarlisle: There is something fishy, the warning doesn't disappear. I'm just looking why. — Ulrike Fischer, Dec 31 '15 at 13:18
@DavidCarlisle: In fontspec-xetex.sty some of the conditionals (e.g. \prg_new_conditional:Nnn \fontspec_check_script:n {TF} set \@tempswatrue. And as some of this code is executed when the aux is read, the label test fails for some fonts. — Ulrike Fischer, Dec 31 '15 at 13:31
@ArTourter My arara instruction is % arara: makechapters: {items: [Chapter1, chapter2,...]} and needs some modifications to my origianl code. It helps creating individual chapters. Here is more information about this rule — Hamed, Dec 31 '15 at 14:13
@UlrikeFischer that sounds like a bug, where's Will when we need him:-) — David Carlisle, Dec 31 '15 at 14:55
@DavidCarlisle: It is certainly a bug, but I wonder a bit now about \if@tempswa. Is it a good idea that the kernel uses it to get the "label state"? It is used in many places, packages and classes and it looks like a small wonder that it doesn't clash more often. — Ulrike Fischer, Dec 31 '15 at 15:01
@Ulrike / David — I'll try remember to switch to an internal Boolean. Happy new year!! — Will Robertson, Dec 31 '15 at 15:07
@WillRobertson or as Ulrike says we could use a dedicated flag in the label test... (one for team list probably) — David Carlisle, Dec 31 '15 at 15:08
@DavidCarlisle: In the long run that sounds like a good idea, but fontspec is probably easier and faster to change. — Ulrike Fischer, Dec 31 '15 at 15:12
@UlrikeFischer normally yes but 2016/01/01 is apparently getting close... — David Carlisle, Dec 31 '15 at 15:23
I'm voting to close this question as off-topic because it is a bug report and meanwhile solved (see comments). — Mensch, Jun 24 '16 at 22:56

Warning message with fonts: Label(s) may have changed. Rerun to get cross-references right

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