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I am trying to include subfiles in a large document, one of the child tex files uses schemes to input .eps files from chemdraw, which includes automatic numbering from the chemstyle package.

This works fine as long as the tex file including the scheme is compiled before any other tex subfile. If it is after another subfile the log just says error and aborts (it doesn't come up with an error message) and the synctex.gz file becomes stuck on (busy).

This is the master tex file:

\documentclass[12pt]{article}
\usepackage[table]{xcolor}
\usepackage{SIunits}

\usepackage[numbers,super,sort&compress,comma]{natbib}
\usepackage[top=2cm, bottom=2cm, left=3cm, right=2cm]{geometry}
\usepackage{textcomp}
\usepackage{graphicx}
\usepackage[runs=2]{auto-pst-pdf}
\usepackage{chemstyle}
\usepackage{booktabs,array}
\usepackage{tabularx}
\usepackage{subcaption}
\usepackage{fancyhdr}
\pagestyle{fancy}
\usepackage{setspace}
\doublespacing

\usepackage[utf8]{inputenc}
\usepackage{subfiles}

\let\stdsection\section
\renewcommand\section{\newpage\stdsection}

\begin{document}

\compound*{RB70, RB76, RB51, RB54, RB55, RB146, RB177, RB156, RB80, RB87, RB168, RB174}


\subfile{Chapter}
\subfile{Experimental}

\section{References}

\bibliographystyle{C:/Users/Ryan/newunsrt}
\bibliography{C:/Users/Ryan/Thesis}



\end{document}

The chapter subfile is mostly just text and figures, nothing fancy. The Experimental tex file has an excerpt below and the master will not work if this is compiled after the chapter tex file by subfiles. If I swap the chapter and experimental subfile commands around, they miraculously work!

Experimental tex file:

\documentclass[master.tex]{subfiles}

\begin{document}
\section{Experimental}

to precipitate formation which was filtered to give the product as an orange solid (38 \milli\gram, 44\% yield). IR (thin film)/cm\textsuperscript{-1} $\nu_{max}$; 3394 br w, 3233 br m, 2933 s, 2875 s, 1692 s, 1646 s, 1546 s, 1307 s, 1195 s, 983 s, 715 s; \textsuperscript{1}H NMR (300 MHz, Methanol-\textit{d$_4$}) $\delta_H$ 6.16 (s, 2H), 3.04-2.94 (m, 4H), 2.47 (s, 6H), 2.44 (s, 6H), 1.81-1.56 (m, 6H);  \textsuperscript{13}C NMR (100 MHz, MeOD) $\delta_C$ 155.56, 148.34, 142.88, 133.23, 123.29, 41.35, 33.07, 29.55, 29.01, 28.59, 17.21, 15.10; HRMS-ESI; [M+H]\textsuperscript{+} calc'd for  C$_{18}$H$_{27}$BN$_3$F$_2$ 334.2266 found; 334.2260.

\begin{center}
\line(1,0){440}
\end{center}

\begin{figure}[ht!]
\begin{center}
\schemeref[TMP1]{RB70}
\includegraphics[width=0.3\textwidth]{Compounds/RB70RhoBNbocpip.eps}
\end{center}
\end{figure}

\end{document}

I know some of the previous compound labels in the master are redundant...

I've tried a few things to fix this but I am stumped so I really appreciate any help you can give! I'm using texmaker on windows :)

closed as unclear what you're asking by user36296, Stefan Pinnow, TeXnician, Troy, Mensch Oct 17 '17 at 12:18

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I've figured this out myself, turns out I had some lines in the preamble which dealt with removing the slant on greek letters and I think a pdfrestore command in here was messing up the eps compiling somehow.

Anyway, my files are compiling as they should and the compound numbering from chemstyle is working. Thought I would answer my own question in case anyone else has the same issue...

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