Prologue
As I am writing (or have written) my Ph.D. dissertation using XeLaTeX, and have also authored several scientific papers using pdfLaTeX, this blog serves as a personal record of the various problems I have encountered when using TeX-based typesetting tools — along with some scripts I created to assist the process.
Scripts
Most of the following scripts (unless otherwise specified) are intended to be saved as .bat files
Compile
This script uses latexmk to compile the dissertation. After each compilation, the user is expected to press any key and compile the .tex file again.
@echo off
:: Turn off command echoing to keep the output clean
:loop
:: This is the start of the loop — it will repeat after each compilation
cls
:: Clear the screen for readability
echo Compiling LZhao.tex with SyncTeX enabled...
:: Compile the LaTeX document using latexmk
:: -xelatex → Use XeLaTeX (a LaTeX engine with Unicode and font support)
:: -bibtex → Run BibTeX to process the bibliography
:: -silent → Suppress most output, including warnings and other verbose messages
:: -synctex=1 → Enable SyncTeX for editor/viewer synchronization (e.g., click in PDF → jump to .tex)
latexmk -xelatex -bibtex -synctex=1 texfile.tex
echo.
echo Press any key to recompile or close this window to exit...
pause >nul
:: Wait for the user to press any key before continuing (">nul" hides the default message)
goto loop
:: Go back to the start of the loop to allow recompilation
Clear
This script clear most of the auxilary files which are generated when compiling a .tex file.
@echo off
title LaTex Cleaner
del /a /f /q /s "*.aux"
del /a /f /q /s "*.bak"
del /a /f /q /s "*.bbl"
del /a /f /q /s "*.bcf"
del /a /f /q /s "*.blg"
del /a /f /q /s "*.dvi"
del /a /f /q /s "*.fdb_latexmk"
del /a /f /q /s "*.fls"
del /a /f /q /s "*.glg"
del /a /f /q /s "*.glo"
del /a /f /q /s "*.gls"
del /a /f /q /s "*.hd"
del /a /f /q /s "*.idx"
del /a /f /q /s "*.ilg"
del /a /f /q /s "*.ind"
del /a /f /q /s "*.ist"
del /a /f /q /s "*.lof"
del /a /f /q /s "*.log"
del /a /f /q /s "*.lot"
del /a /f /q /s "*.out"
del /a /f /q /s "*.run.xml"
del /a /f /q /s "*.sav"
del /a /f /q /s "*.synctex.gz"
del /a /f /q /s "*.synctex\(busy\)"
del /a /f /q /s "*.thm"
del /a /f /q /s "*.toc"
del /a /f /q /s "*.slg"
del /a /f /q /s "*.slo"
del /a /f /q /s "*.sls"
del /a /f /q /s "*.toe"
del /a /f /q /s "*.xdy"
del /a /f /q /s "*.listing"
XeLaTeX
xdvipdfmx
xdvipdfmx:warning: Trying to include PDF file with version (1.7), which is newer than current output PDF setting (1.5).
This warning indicates that a PDF file being included (e.g., via \includegraphics) uses a newer PDF version (e.g., 1.7) than the version of the PDF that XeLaTeX is set to produce (e.g., 1.5).
To resolve this, either downgrade the input PDF version, or instruct hyperref to set the output PDF version to match (or exceed) the input file’s version:
\usepackage[pdfversion=1.7]{hyperref}
xdvipdfmx:warning: Can’t begin an annotation when one is pending.
The full warning is:
[60
xdvipdfmx:warning: Can't begin an annotation when one is pending.
xdvipdfmx:warning: Interpreting special command bann (pdf:) failed.
xdvipdfmx:warning: >> at page="60" position="(228.335, 439.578)" (in PDF)
xdvipdfmx:warning: >> xxx "pdf:bann<</Type/Annot/Subtype/Link/Border[0 0 0]/H/I/C[1 0 0..."
xdvipdfmx:warning: >> Reading special command stopped around >><</Type/Annot/Subtype/Link/Border[0 0 0]/H/I/C[1 0 0]/A<</S/...<<
][61
xdvipdfmx:warning: Tried to end an annotation without starting one!
xdvipdfmx:warning: Interpreting special command eann (pdf:) failed.
xdvipdfmx:warning: >> at page="61" position="(85.656, 272.291)" (in PDF)
xdvipdfmx:warning: >> xxx "pdf:eann"
]
where 60 and 61 are pages that encountered the warning. The output figures are clickable and refer to some incorrect targets.
Here’s an example that caused the warning in my case:
\begin{figure}[p]
\centering
\includegraphics[width=0.8\textwidth]{./Figures/ccc.eps}
\caption{
xxx\ref{fig:aaa}xxx
}
\label{fig:ccc}
\end{figure}
\begin{figure}[p]
\centering
\includegraphics[width=0.8\textwidth]{./Figures/ddd.eps}
\caption{
xxx\ref{fig:bbb}xxx
}
\label{fig:ddd}
\end{figure}
This issue likely arises when xdvipdfmx tries to handle consecutive figure captions with \ref links and insufficient vertical spacing, which disrupts the internal annotation state machine.
The simples solution for this problem is to add vertical gap between two figures, like:
\begin{figure}[p]
\centering
\includegraphics[width=0.8\textwidth]{./Figures/ccc.eps}
\caption{
xxx\ref{fig:aaa}xxx
}
\label{fig:ccc}
\end{figure}
\vspace{1cm}
\begin{figure}[p]
\centering
\includegraphics[width=0.8\textwidth]{./Figures/ddd.eps}
\caption{
xxx\ref{fig:bbb}xxx
}
\label{fig:ddd}
\end{figure}
