Conflicts between subfiles and caption packages

Question

I am writing a paper that has an online appendix. The paper and appendix reference figures in each other. I'd like to be able to compile each of the documents as a separate .pdf file and maintain the figure referencing. The subfiles package seems to work pretty well for this. But, there is a tiny flaw in that it seems to have difficulties when I also use the caption package in order to modify, for example, how figure numbers appear. In essence, what happens is that if I also load the caption package, then the hyperlinks in my appendix no longer work properly. When I compile the document, I get the following Warning:

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

Unfortunately, if I re-run the compilation, it breaks other references. Below is a minimal working example with more specific explanation of the procedure I'm trying to follow.

Main.tex

\documentclass{report}
\usepackage{subfiles}
\usepackage{xr-hyper}
\usepackage{hyperref}
\usepackage[notablist,nofiglist,nomarkers]{endfloat}

\usepackage{caption}

\begin{document}


\subfile{Body.tex}

\setcounter{page}{1}
\setcounter{figure}{0}
\setcounter{postfigure}{0}

\renewcommand{\thepostfigure}{\Alph{section}.\arabic{postfigure}}
\renewcommand{\thefigure}{\Alph{section}.\arabic{figure}}


\subfile{Appendix.tex}

\end{document}

Body.tex

\documentclass[Main.tex]{subfiles}
\begin{document}


\section{Section 1}
\label{sec:Section1}

\begin{figure}
\centering\rule{1cm}{1cm}
\caption{Body Figure 1}
\label{body_fig1}
\end{figure}



As I show in \autoref{fig1} in \autoref{sec:Online_Appendix} of the appendix ...


\processdelayedfloats


\end{document}

Appendix.tex

\documentclass[Main.tex]{subfiles}
\begin{document}

\pagebreak
\appendix
\section{Online Appendix}
\label{sec:Online_Appendix}


My discussion in \autoref{sec:Section1} is informed by \autoref{fig1} and \autoref{fig2} and \autoref{fig3}.


\begin{figure}
\centering\rule{1cm}{1cm}
\caption{Appendix Figure 1}
\label{fig1}
\end{figure}


\pagebreak

\begin{figure}
\centering\rule{1cm}{1cm}
\caption{Appendix Figure 2}
\label{fig2}
\end{figure}

\pagebreak

\begin{figure}
\centering\rule{1cm}{1cm}
\caption{Appendix Figure 3}
\label{fig3}
\end{figure}


\end{document}

Work Flow

1. I first compile Main.tex.
2. I then comment out the \subfile{Body.tex} and recompile Main.tex. This generates the proper text for the appendix, but the hyperlinks to the figures go to the wrong places in the document when clicked. This is where I get the warning about labels having changed.
3. If I recompile Main.tex again, the hyperlinks to the figures in the appendix now work, but the reference to the section in Body.tex now appears as ??

Comments

• All of this works fine if I don't have the caption package enabled.
• If I just try to compile either Body.tex or Appendix.tex separately, the cross references don't work correctly, which is why I use the procedure with the multiple separate compilations of Main.tex.

Answer 1

You are missing the external document parts from https://tex.stackexchange.com/a/378163/36296. If you want a reference in a subfile to another subfile, you have to specify this external document:

\documentclass{report}
\usepackage{subfiles}
\usepackage{xr-hyper}
\usepackage{hyperref}
\usepackage[notablist,nofiglist,nomarkers]{endfloat}
\usepackage{xstring}

\usepackage{caption}

\begin{document}


\subfile{body.tex}

\setcounter{page}{1}
\setcounter{figure}{0}
\setcounter{postfigure}{0}

\renewcommand{\thepostfigure}{\Alph{section}.\arabic{postfigure}}
\renewcommand{\thefigure}{\Alph{section}.\arabic{figure}}


\subfile{appendix.tex}

\end{document}

---

% !TeX root = body.tex
\documentclass[main.tex]{subfiles}

\IfEq{\jobname}{\detokenize{main}}{}{%
    \externaldocument{appendix}
}

\begin{document}


\section{Section 1}
\label{sec:Section1}

\begin{figure}
\centering\rule{1cm}{1cm}
\caption{Body Figure 1}
\label{body_fig1}
\end{figure}



As I show in \autoref{fig1} in \autoref{sec:Online_Appendix} of the appendix ...


\processdelayedfloats


\end{document}

---

% !TeX root = appendix.tex
\documentclass[main.tex]{subfiles}

\IfEq{\jobname}{\detokenize{main}}{}{%
    \externaldocument{body}
}

\begin{document}

\pagebreak
\appendix
\section{Online Appendix}
\label{sec:Online_Appendix}


My discussion in \autoref{sec:Section1} is informed by \autoref{fig1} and \autoref{fig2} and \autoref{fig3}.


\begin{figure}
\centering\rule{1cm}{1cm}
\caption{Appendix Figure 1}
\label{fig1}
\end{figure}


\pagebreak

\begin{figure}
\centering\rule{1cm}{1cm}
\caption{Appendix Figure 2}
\label{fig2}
\end{figure}

\pagebreak

\begin{figure}
\centering\rule{1cm}{1cm}
\caption{Appendix Figure 3}
\label{fig3}
\end{figure}


\end{document}

As the subfiles cyclically depend on each other, compilation order for the first compilation may be a bit tricky, but compiling body, appendix, body, appendix should probably do.