Problems rendering to PDF

[jpmorr]

Hi,

I've put together my first book project and I want to render it to both html and pdf. I've set up my _quarto.yml as such:

project:
  type: book

book:
  title: "my_book"

  author:
   - Me

  Affiliations:
   - Work
   
  date: "10/08/2022"
  
  chapters:
    - index.qmd
    - part: "Model Details"
      chapters:
      - intro.qmd
      - c2.qmd
      - c3.qmd
      - c4.qmd
      - c5.qmd
      - c6.qmd
    - part: "Examples"
      chapters:
        - example_problem.qmd
        - Example1_results.qmd
    - references.qmd
  appendices:
    - A1.qmd
    - A2.qmd
    - A3.qmd
    - A4.qmd

  page-navigation: true
  page-footer: 
    center: "Copyright 2021, Norah Jones" 
    left:
      - icon: github
        href: https://github.com/
    right: 
      - icon: twitter 
        href: https://twitter.com/ 

downloads: [pdf]
        
bibliography: references.bib
csl: elsevier-with-titles-alphabetical.csl

format:
  html:
    theme: cosmo
  pdf: 
    documentclass: book
    lof: true
    lot: true
    toc: true    
    geometry:
      - top=30mm
      - left=20mm
      - heightrounded
    hyperrefoptions:
      - linktoc=all
    colorlinks: true
    linkcolor: "blue"
    biblio-style: apalike
    keep-tex: true

latex-auto-install: true

I'm using VS Code on Windows 11

running xelatex - 1
  This is XeTeX, Version 3.141592653-2.6-0.999994 (MiKTeX 22.7.30) (preloaded format=xelatex.fmt)
   restricted \write18 enabled.
  entering extended mode


compilation failed- missing packages (automatic installed disabled)
Extra alignment tab has been changed to \cr.
<recently read> \endtemplate

l.454 ... & \cdot & -k_1 & \cdot & \cdot & \cdot &
                                                   \cdot & \cdot \\

see D:\Workspace\quarto\my_book\index.log for more information.

The last few entries in the index.log file are:

LaTeX Warning: Reference `fig-Bond_FM' on page 10 undefined on input line 425.

File: ./images/Bond_FM.png Graphic file (type bmp)
<./images/Bond_FM.png>
! Extra alignment tab has been changed to \cr.
<recently read> \endtemplate 
                             
l.454 ... & \cdot & -k_1 & \cdot & \cdot & \cdot &
                                                   \cdot & \cdot \\ 

Which isn't too helpful, but it seems to fail on the following equation:

\begin{equation}\protect\hypertarget{eq-StiffnessMatrix}{}{
\left[ K \right] =
\begin{bmatrix} 
k_1 & \cdot & \cdot & \cdot & \cdot & \cdot & -k_1 & \cdot & \cdot & \cdot & \cdot & \cdot \\
 \cdot & k_2 & \cdot & \cdot & \cdot & k_3 & \cdot & -k_2 & \cdot & \cdot & \cdot & k_3 \\
 \cdot & \cdot & k_2 & \cdot & -k_3 & \cdot & \cdot & \cdot & -k_2 & \cdot & -k_3 & \cdot \\
 \cdot & \cdot & \cdot & k_4 & \cdot & \cdot & \cdot & \cdot & \cdot & -k_4 & \cdot & \cdot \\
 \cdot & \cdot & -k_3 & \cdot & k_5 & \cdot & \cdot & \cdot & k_3 & \cdot & k_6 & \cdot \\
 \cdot & k_3 & \cdot & \cdot & \cdot & k_5 & \cdot & -k_3 & \cdot & \cdot & \cdot & k_6 \\
-k_1 & \cdot & \cdot & \cdot & \cdot & \cdot & k_1 & \cdot & \cdot & \cdot & \cdot & \cdot \\
 \cdot & -k_2 & \cdot & \cdot & \cdot & k_3 & \cdot & k_2 & \cdot & \cdot & \cdot & -k_3 \\
 \cdot & \cdot & -k_2 & \cdot & k_3 & \cdot & \cdot & \cdot & k_2 & \cdot & k_3 & \cdot \\
 \cdot & \cdot & \cdot & -k_4 & \cdot & \cdot & \cdot & \cdot & \cdot & k_4 & \cdot & \cdot \\
 \cdot & \cdot & -k_3 & \cdot & k_6 & \cdot & \cdot & \cdot & k_3 & \cdot & k_5 & \cdot \\
 \cdot & k_3 & \cdot & \cdot & \cdot & k_6 & \cdot & -k_3 & \cdot & \cdot & \cdot & k_5 
\end{bmatrix}
}\label{eq-StiffnessMatrix}\end{equation}

Not quite sure why it's failing here for the latex but not html render. Any ideas?

[cscheid]

We need to see the actual qmd files to give a better answer. Is that equation typed in LaTeX in your .qmd file? It might be because math expressions are evaluated at runtime through MathJax, and so you won't see a render error in html.

[jpmorr]

I think you're correct - overleaf just complained when I tried to compile a blank document with it. Will investigate after dinner.

[jpmorr]

It seems to be not loading the required latex package for a matrix. In overleaf I just needed to add the following package: \usepackage{amsmath}. How do I make quarto find this package?

I've tried adding this to the yml file but it doesn't help:

    include-in-header: 
          text: |
            \usepackage{amsmath}

[rgaiacs]

@jpmorr Consider the following minimal working example:

---
title: "math"
format:
  pdf:
    keep-tex: true
---

Example $x$ and $$x^2 + x + 1$$.

When I render the document, I get a .tex file that starts with

% Options for packages loaded elsewhere
\PassOptionsToPackage{unicode}{hyperref}
\PassOptionsToPackage{hyphens}{url}
\PassOptionsToPackage{dvipsnames,svgnames,x11names}{xcolor}
%
\documentclass[
  letterpaper,
  DIV=11,
  numbers=noendperiod]{scrartcl}

\usepackage{amsmath,amssymb}
\usepackage{lmodern}
\usepackage{iftex}

The LaTeX amsmath is included in the LaTeX template used by Quarto. Now, you should check

1. Is the amsmath package included in the .tex that you generate. You don't need the include-in-header.
2. Does your LaTeX installation have the amsmath package?
3. Is your local copy of amsmath package updated?

In the past, I had co-authors complaining they couldn't compile my .tex only to find out they didn't updated their LaTeX installation in 2 years.

[jpmorr]

Thanks for the pointers @rgaiacs. I'll try to answer your questions first:

1. You are correct that the amsmath should be included and opening my .tex file I can see it on listed ther eon line 9, so that part is OK.
2. Yes, my LaTeX installation miktex has the ams packages installed.
3. While it was not immediately up to date ( maybe the last 6 months) I updated miktex today and it did update the amsmath package, it does not help.

I've created a bare minimum working example:

1. Create new book project with quarto: quarto create-project mybook --type book
2. Create any equation in the intro.qmd file

# Introduction

This is a book created from markdown and executable code.

See @knuth84 for additional discussion of literate programming.

Example $x$ and $x^2 + x + 1$.

$$
k_1 = \dfrac{E_b A_b}{L_b}
$$ {#eq-k1}

3. Use quarto to render quarto render --to all

4. PDF and html files are created as expected.

5. Either replace existing equations or simply add the offending equation to intro.qmd:

# Introduction

This is a book created from markdown and executable code.

See @knuth84 for additional discussion of literate programming.

Example $x$ and $x^2 + x + 1$.

$$
k_1 = \dfrac{E_b A_b}{L_b}
$$ {#eq-k1}

$$
\left[ K \right] =
\begin{bmatrix} k_1 & \cdot & \cdot & \cdot & \cdot & \cdot & -k_1 & \cdot & \cdot & \cdot & \cdot & \cdot \\
\cdot & k_2 & \cdot & \cdot & \cdot & k_3 & \cdot & -k_2 & \cdot & \cdot & \cdot & k_3 \\
\cdot & \cdot & k_2 & \cdot & -k_3 & \cdot & \cdot & \cdot & -k_2 & \cdot & -k_3 & \cdot \\
\cdot & \cdot & \cdot & k_4 & \cdot & \cdot & \cdot & \cdot & \cdot & -k_4 & \cdot & \cdot \\
\cdot & \cdot & -k_3 & \cdot & k_5 & \cdot & \cdot & \cdot & k_3 & \cdot & k_6 & \cdot \\
\cdot & k_3 & \cdot & \cdot & \cdot & k_5 & \cdot & -k_3 & \cdot & \cdot & \cdot & k_6 \\
-k_1 & \cdot & \cdot & \cdot & \cdot & \cdot & k_1 & \cdot & \cdot & \cdot & \cdot & \cdot \\
\cdot & -k_2 & \cdot & \cdot & \cdot & k_3 & \cdot & k_2 & \cdot & \cdot & \cdot & -k_3 \\
\cdot & \cdot & -k_2 & \cdot & k_3 & \cdot & \cdot & \cdot & k_2 & \cdot & k_3 & \cdot \\
\cdot & \cdot & \cdot & -k_4 & \cdot & \cdot & \cdot & \cdot & \cdot & k_4 & \cdot & \cdot \\
\cdot & \cdot & -k_3 & \cdot & k_6 & \cdot & \cdot & \cdot & k_3 & \cdot & k_5 & \cdot \\
\cdot & k_3 & \cdot & \cdot & \cdot & k_6 & \cdot & -k_3 & \cdot & \cdot & \cdot & k_5 
\end{bmatrix}
$$ {#eq-StiffnessMatrix}

This now breaks quarto with the following message:

running xelatex - 1
  This is XeTeX, Version 3.141592653-2.6-0.999994 (MiKTeX 22.7.30) (preloaded format=xelatex.fmt)
   restricted \write18 enabled.
  entering extended mode


compilation failed- missing packages (automatic installed disabled)
Extra alignment tab has been changed to \cr.
<recently read> \endtemplate

l.212 ... & \cdot & -k_1 & \cdot & \cdot & \cdot &
                                                   \cdot & \cdot \\

Going through the generated tex file I think I see the problem now:

Example \(x\) and \(x^2 + x + 1\).

\begin{equation}\protect\hypertarget{eq-k1}{}{
k_1 = \dfrac{E_b A_b}{L_b}
}\label{eq-k1}\end{equation}

\begin{equation}\protect\hypertarget{eq-StiffnessMatrix}{}{
\left[ K \right] =
\begin{matrix} k_1 & \cdot & \cdot & \cdot & \cdot & \cdot & -k_1 & \cdot & \cdot & \cdot & \cdot & \cdot \\
\cdot & k_2 & \cdot & \cdot & \cdot & k_3 & \cdot & -k_2 & \cdot & \cdot & \cdot & k_3 \\
\cdot & \cdot & k_2 & \cdot & -k_3 & \cdot & \cdot & \cdot & -k_2 & \cdot & -k_3 & \cdot \\
\cdot & \cdot & \cdot & k_4 & \cdot & \cdot & \cdot & \cdot & \cdot & -k_4 & \cdot & \cdot \\
\cdot & \cdot & -k_3 & \cdot & k_5 & \cdot & \cdot & \cdot & k_3 & \cdot & k_6 & \cdot \\
\cdot & k_3 & \cdot & \cdot & \cdot & k_5 & \cdot & -k_3 & \cdot & \cdot & \cdot & k_6 \\
-k_1 & \cdot & \cdot & \cdot & \cdot & \cdot & k_1 & \cdot & \cdot & \cdot & \cdot & \cdot \\
\cdot & -k_2 & \cdot & \cdot & \cdot & k_3 & \cdot & k_2 & \cdot & \cdot & \cdot & -k_3 \\
\cdot & \cdot & -k_2 & \cdot & k_3 & \cdot & \cdot & \cdot & k_2 & \cdot & k_3 & \cdot \\
\cdot & \cdot & \cdot & -k_4 & \cdot & \cdot & \cdot & \cdot & \cdot & k_4 & \cdot & \cdot \\
\cdot & \cdot & -k_3 & \cdot & k_6 & \cdot & \cdot & \cdot & k_3 & \cdot & k_5 & \cdot \\
\cdot & k_3 & \cdot & \cdot & \cdot & k_6 & \cdot & -k_3 & \cdot & \cdot & \cdot & k_5 
\end{matrix}
}\label{eq-StiffnessMatrix}\end{equation}

quarto / pandoc is not correctly converting the equation - it's creating it as a {matrix} instead of a {bmatrix} from amsmath as expected. So if it compiled, it could generate the wrong output - missing brackets.

Anyway, this got me reading the amsmath documentation and I found the solution to the problem in the amsmath documentation in a footnote after section 4.1 on matrices:

" The maximum number of columns in a matrix is determined by the counter MaxMatrixCols (normal value = 10), which you can change if necessary using LATEX’s setcounter or \addtocounter commands."

So I've gone back and added the following into the yml:

format:
  html:
    theme: cosmo
  pdf:
    documentclass: scrreprt
    keep-tex: true
    include-in-header: 
          text: |
            \setcounter{MaxMatrixCols}{20}

And this finally makes the minimal example and full book compile!! 😄

It seems other latex editors and tools must already be setting this value for the user automatically if they come across a large matrix as I didn't have to specify in either overleaf or texstudio.

[rgaiacs]

WOW @jpmorr I'm impressed with your debugging skills. 👍 I'm glad that you found the solution.

[jpmorr]

There is a limit on the number of columns (which is 10 by default) in a matrix. Need to send a command to change the default number of columns allowed in a matrix to enable it to compile. See amsmath package documentation.

    include-in-header: 
          text: |
            \setcounter{MaxMatrixCols}{20}