Error: Environment env-<guid> undefined.

[colindean]

I'm seeing this on a project to which I'm attempting to add pandoc-latex-admonition:

$ pandoc pandoc-latex-admonition-sample.txt -f markdown --defaults testconfig.yaml -o output.pdf
Error producing PDF.
! LaTeX Error: Environment env-fd8d3a40-b6dc-4916-a88f-6e8cf64f93f4 undefined.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.72 ...{env-fd8d3a40-b6dc-4916-a88f-6e8cf64f93f4}

I seem able to reproduce it against the example file. It seems related to adding glossaries.

What seems like the minimal files necessary to reproduce this: https://gist.github.com/colindean/ffd9e24299582f72af8de1e385e6df60

I'm running pandoc 2.9.1 in my builds (a specific container built for this) but I seem able to reproduce it against pandoc 2.10.1 as well.

$ pandoc --version
pandoc 2.9.1
Compiled with pandoc-types 1.20, texmath 0.12, skylighting 0.8.3
Default user data directory: /root/.local/share/pandoc or /root/.pandoc
Copyright (C) 2006-2019 John MacFarlane
Web:  http://pandoc.org
This is free software; see the source for copying conditions.
There is no warranty, not even for merchantability or fitness
for a particular purpose.

I'm running this using pandocker with basically

alias pandoc="docker run -it --rm -v \$(pwd):/pandoc dalibo/pandocker:stable"

Outputting latex instead of pdf shows that the environments are matched.

I'm very eager to get this working. It appears that #2 and #6 delved into this but neither author posted a solution.

[colindean]

I set up pandoc and pandoc-latex-admonition from scratch

• pandoc 2.11.3
• pandoc-latex-admonition 1.3.1
• texlive-latex-extra 2017.20180305-2
• pdfTeX 3.14159265-2.6-1.40.18

[colindean]

I poked around a bit and can't figure it out.

[hauptanja]

I am having the same problem.

[chdemko]

Can you post steps to reproduce the issue?

[chdemko]

It seems that is issue comes from pandoc itself (jgm/pandoc#3139 and pandoc-discuss) which overrides the LaTeX header. I suggest not using the --include-in-header option and to add

header-includes:
- |
  ```{=latex}
  \usepackage{glossaries}
  \setacronymstyle{long-short-desc}
  \makenoidxglossaries
  \include{glossary}
  ```

in the metadata block of pandoc-latex-admonition-sample.txt.

[hauptanja]

docker run --rm --platform linux/amd64 --volume "pwd:/pandoc" --user id -u:id -g dalibo/pandocker --listings -V geometry:margin=1in --from markdown --template=default.tex -s --pdf-engine=lualatex --toc --toc-depth=2 --top-level-division=chapter --filter pandoc-latex-admonition -f markdown-implicit_figures ./manual_final.md -o ./manual_final.pdf

template.tex

\documentclass[a4, 12pt]{report}
\usepackage[margin=1in]{geometry}
\usepackage{fontspec}
\usepackage{hyperref}
% \usepackage{adjustbox}
\usepackage{float}
\usepackage{fancyhdr}
\usepackage{titlesec}
\usepackage{tocloft}
\usepackage{titling}
\usepackage{longtable}
\usepackage{listings}
% \usepackage{tabularx}
% \usepackage{booktabs}
% \usepackage{fvextra}
\usepackage{xcolor, tcolorbox, footnote, ifthen} % for pandoc-latex-admonition

\providecommand{\tightlist}{%
  \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}%
}
\setlength{\emergencystretch}{3em} % prevent overfull lines

% $if(listings)$
\usepackage{listings}
\newcommand{\passthrough}[1]{#1}
% $endif$

$if(tables)$
\usepackage{longtable,booktabs,array}
$if(multirow)$
\usepackage{multirow}
$endif$
\usepackage{calc} % for calculating minipage widths
$endif$

\restylefloat{figure}
\setmainfont{Lato} 
% \setsansfont{Liberation Sans}
\setmonofont{Liberation Sans}

% Set up the page style for the document
\fancypagestyle{fancy}{%
  \fancyhf{} % Clear header and footer
  \renewcommand{\headrulewidth}{0pt} % Remove header rule
  \renewcommand{\footrulewidth}{0pt} % Remove footer rule
  \lhead{\hrulefill} % Add horizontal line to header
  \rhead{} % Clear right header
  \cfoot{\thepage} % Page number in the center of the footer
}

% Chapter formatting
\titleformat{\chapter}[display]
  {\normalfont\large\bfseries}{}{0pt}{\LARGE}

% Set up the table of contents formatting
\renewcommand{\cftchapdotsep}{\cftdotsep} % Use dots for chapters
\renewcommand{\cftchapleader}{\cftdotfill{\cftchapdotsep}} % Use dots for chapter entries
\renewcommand{\cftsecleader}{\cftdotfill{\cftdotsep}}
\setcounter{tocdepth}{2}

$if(graphics)$
\usepackage{graphicx}
  % Redefine \includegraphics so that, unless explicit options are
  % given, the image width will not exceed the width or the height of the page.
  % Images get their normal width if they fit onto the page, but
  % are scaled down if they would overflow the margins.
  \makeatletter
  \def\ScaleWidthIfNeeded{%
   \ifdim\Gin@nat@width>\linewidth
      \linewidth
    \else
      \Gin@nat@width
    \fi
  }
  \def\ScaleHeightIfNeeded{%
    \ifdim\Gin@nat@height>0.9\textheight
      0.9\textheight
    \else
      \Gin@nat@width
    \fi
  }
\makeatother

\setkeys{Gin}{width=\ScaleWidthIfNeeded,height=\ScaleHeightIfNeeded,keepaspectratio}%
$endif$

\begin{document}

% Cover page
\begin{titlepage}
  \centering
  \includegraphics[width=0.5\textwidth]{biocoded-head.png} % Replace with your logo image

  \vspace{2cm}
  
  \Large\textbf{$title$}

  \Large\textbf{$revision.number$}

  \vspace{1cm}

  \textbf{$subtitle$}

  \vspace{0.5cm}

  \small\textbf{$companyname$}

  \small\textbf{$companyaddress$}

  \small\textbf{$officeaddress$}

  \vspace{0.5cm}

  \small\textbf{$contact$}

  \vspace{0.5cm}

  \small\textbf{$date$}

  % Clear the page for the next content
  \clearpage
\end{titlepage}


% Table of Contents
\tableofcontents
\clearpage

$body$

\end{document}

manual_final.md

---
title: '{}'
revision:
  number: '0'
subtitle: `Subtitle '
companyname: `...'
companyaddress: `....'
officeaddress: `....'
contact: 'Contact E-mail: ...'
date: {}

papersize: a4
toc: true
mainfont: Lato
geometry: margin=1in

pandoc-latex-admonition:
  - color: gray
    classes: [admonition]
---
Blabla...

~~~admonition
This is important content
~~~