28  Trouble and troubleshooting

28.1 Paragraph starts with ‘(1)’ or ‘1.’ or some other list code

Problem. you have a paragraph or blockquote starting with (1) or 2) or 3.. Pandoc thinks it’s a list, but it’s not.

Solution. Escape the parenthesis or dot that follows the number.

I TYPE I GET 
(1) This is interpreted
as a list item.

3. And so is this.
  1. This is interpreted as a list item.
  1. And so is this.
 
(1\) This isn't interpreted
as a list item.

3\. This isn't either.

(1) This isn’t interpreted as a list item.

3. This isn’t either.

28.2 If PDF generation doesn’t work

Make sure first that you’ve checked the advice in the “how to produce outputs” sections.

PDF generation happens in two stages. Identify which one fails:

  • Markdown to LaTeX (the Pandoc stage)
  • or LaTeX to PDF (the LaTeX stage)

You do so by trying to generate a LaTeX (.tex) output. If that fails, there’s an error at the Pandoc stage, otherwise (more commonly, unfortunately) the error is at the latex stage.

Pandoc-stage errors are mostly due to:

  1. Faulty YAML metadata.
    1. YAML parse exception at line 453.. your YAML is not well formatted. See the metadata section.
    2. Even if you don’t get the YAML parse error, there might be some formatting error around line breaks or identation. Check multiline fields and nested fields of maps/lists.
    3. Some YAML value isn’t correct and makes a filter crash.
  2. File not found. File not found in resource path error, see below.
  3. A bug in one of the “filters” that we use to handle various typesetting tasks (e.g. statements). You will see the name lua in the error message.
  4. Faulty LaTeX template. Cannot compile the template error. There’s an error in the house template.

LaTeX stage errors are due to a multitude of causes. You can learn more about the error by running your pdf engine on the LaTeX output:

lualatex article.tex

For lualatex; replace with pdflatex or xelatex depending on your setup.

Once you run LaTeX a detailed log of its action rolls out—faster than you can read. The error message will be close to the end and look like this:

Error/Warning (...) Error: MESSAGE

Type  H <return>  for immediate help.
 ...                                              
                                                  
l.3984       {See the manual for further details.}

The l.3984 is the line of the LaTeX file where the error arose. (Not necessarily the line that caused it! The cause might be earlier in the code, though not later.) You can go to that location in your LaTeX file and investigate.

You can place the LaTeX run log in a file if you want to examine it in a text editor rather than the terminal:

lualatex article.tex > latex_log.txt

28.3 Word manuscript with many symbols (phi, psy, greek letters, logical symbols,).

If the symbols aren’t in MS Word Equations, they will be preserved as is in markdown - and the document won’t work. All the symbols have to converted into LaTeX formulas. A tip:

  • Use search and replace in RStudio to convert each symbol in its > LaTeX equivalent.

  • Then go through the document to enclose each of them in $...$ (to > indicate maths formulas).

28.4 Reverse conversion .md -> .tex

I want I type LaTex

Basic

(Smith, 2012)

(Smith, 2012, 2015)

(Smith 2012; Jones 2015)

(Smith 2012, 205)

(see Smith 2012, 205)

(Smith 2012, 205-210, 235)

(Smith 2012, 28; Jones 2015, 2017)

(see Smith 2012, 28; comp. Jones 2015, 28; also Jones 2017, 45-58)

[@Smith2012]

[@Smi th2012;@Smith2015]

[@Smi th2012;@Jones2015]

[@Smith2012, 205]

[see @Smith2012, 205]

[@Smith2012, 205--210, 235]

[@Smith2012, 28; @Jones2015; @Jones2017]

[see @Smith2018, 28; comp. @Jones2015, 28; also @Jones2017, 45--48].

\citep{smith:2012}

\citep{sm ith:2012,smith:2015}

\citep{sm ith:2012,jones:2015}

\cite p[205]{smith:2012}

\citep[see
][205]{smith:2012}

\citep[205--2 10,235]{smith:2012}

(Smith \citeyea r[28]{smith:2012}; Jones \citeyear{jon es:2015,jones:2017})

(see Smith \citeyea r[28]{smith:2012}; comp. Jones \citeyea r[28]{jones:2015}; also Jones \citeyear[45 --58]{jones:2017})

Inline

Smith (2012) says that

Smith (2012, 205) says that

Smith (2012; 2015, 205) says that

Peregrin & Svoboda (2013, 2016, 2017, and also Read, 2018)

Alternatively, you can type the name and use year-only:

Smith (2012; 2015)

@Smith2012 says that

@Smith2012 [205] says that

@Smith2012 [@Smith2015, 205] says that

@pe regrin-svoboda:2013a [@pe regrin-svoboda:2016;

@pe regrin-svoboda:2017; and also @read_s:2000]

Smith [-@Smith2012, @Smith2015]

\citet{smith:2012} says that

\cite t[205]{smith:2012} says that

Smith (\c iteyear{smith:2012}, \citeyea r[205]{smith:205}) says that

\citet[][and also Read \citeyear{r ead_s:2000}]{peregr in-svoboda:2013,pere grin-svoboda:2016,pe regrin-svoboda:2017}

Peregrin \& Svoboda (\citeyear{peregri n-svoboda:2013,pereg rin-svoboda:2016,per egrin-svoboda:2017}, and also Read \ci teyear{read_s:2000})

Year only

Smith makes an outrageous claim (2015, 277).

Smith keeps repeating himself (2012, 2013, 2014, 2015).

Smith said this in a few places (2012, 20; 2013, 30)

Smith makes an outrageous claim [-@Smith2015, 277].

Smith keeps repeating himself [-@Smith2012; @Smith2013; @Smith2014; @Smith2015].

Smith said this in a few places [-@Smith2012, 20; @Smith2013, 30].

Smith makes an outrageous claim (\citeyear
[277]{smith:2015}).

Smith keeps repeating himself (\citeyear{smith :2012,smith:2013,smi th:2014,smith:2015})

Smith said this in a few places (\citeyea r[29]{smith:2012}, \citeyear [30]{smith:2013}).

28.5 File not found in resource path

File mydefaults.yaml not found in resource path

The file mydefaults.yaml is absent or not at the place expected. Check whether the relative locations of your article, master and template are correct.

File  not found in resource path

Pandoc is looking for a file with no name. Check if you don’t have an emtpy bibliography field in the metadata.

28.6 HTML/MathJax: Math-mode letter in heading not showing

PROBLEM: a Math-mode letter (e.g. \(\alpha\)) is not showing in a heading in HTML/MathJax output.

SOLUTION. Is your CSS using a font variant, e.g. small-caps? Make sure Spans of the math-inline class are in regular shape and variant.

28.7 Missing character

[WARNING] Missing character: There is no SPECIAL-CHAR (U+2192) in font FONT

Means that your markdown file include a character SPECIAL-CHAR that is not available in the font you use. Typically, SPECIAL-CHAR is a symbol or character from non-latin languages. Note that you might not see anything where SPECIAL-CHAR is above, if the character in question is a (special kind of) space or if it’s not present in the font in which this warning is printed.

Solution: if SPECIAL-CHAR is visible you can copy it, and search it in your markdown file. Remove it and if needed replace it with some character that is present in your font. Typically, this involves replacing a unicode symbol (a right arrow) by its LaTeX equivalent, e.g. \(\rightarrow\).

Solution: if SPECIAL-CHAR is not visible, look up the unicode number (e.g. U+2192 online) to see what character is it, and hunt it down in your markdown manuscript.

28.8 YAML Parse exception

Error message: PandocParseError "YAML parse exception at line 2, column 2:\nmapping values are not allowed in this context"

Solution: this is probably due to several --- lines in your source markdown. The text in between might be interpreted as an additional YAML metadata block by Pandoc. Replace them with a longer dash sequence, e.g ------.

28.9 attempt to compare nil with number

Error:

warning  (node filter): error: ...e/2022/texmf-dist/tex/generic/babel/babel-bid
i-basic.lua:155: attempt to compare nil with number

This bug can be produced by a statement with a custom label containing an uppercase letter followed by a dash, such as:

::: statement
__L-a__. This statement might generate an error!
:::

Fix. Surround the dash with spaces

::: statement
__L - a__. This will not generate an error.
:::

A longer dash probably looks better:

::: statement
__L -- a__. This will not generate an error.
:::

28.10 Hard-coded LaTeX table: Undefined control sequence

We hard-coded a complex LaTeX table but used markdown to include a link target in the caption:

::::: {.only-in-format .latex}

`\begin{longtable}{ccc}`{=latex}
`\caption{`{=latex}Numbers to prove [this idea]{#idea}.`}\\`{=latex}




``` {=latex}
 \hline
    header & header & header \\
  \hline
  ... table rows \\
 \hline
\end{longtable}
```




:::::

We got a “Undefined control sequence” for an obscure command (HyperRaiseLinkLength) that doesn’t appear in the pandoc-generated LaTeX. The cause is that Pandoc inserts a \phantomsection command before the link target:

\begin{longtable}{ccc}
\caption{Numbers to prove \phantomsection\label{idea}{#idea}.}

Which cannot be inserted within table captions.

Solution. Redefine \phantomsection to nothing (or \relax) within the scope of this table. Note that we wrap the entire table within {...} to ensure that \renewcommand only affects this table, not the rest of the document:

::::: {.only-in-format .latex}





``` {=latex}
{
\renewcommand{\phantomsection}{}
\begin{longtable}{ccc}
```




`\caption{`{=latex}Numbers to prove [this idea]{#idea}.`}\\`{=latex}




``` {=latex}
 \hline
    header & header & header \\
  \hline
  ... table rows \\
 \hline
\end{longtable}
```




:::::

28.11 A list of things that cause trouble

Some hurdles that beginning copyeditors typically face.

28.11.1 Visual editor RStudio

  • Does not preserve numbered examples code (all processed).

  • Tables: Doesn’t preserve code (not pipe format -> loss of cell > alignment)

  • Interprets \[ and \] as display maths.

    • Solution: do not escape the [ ]. Only possible problem: it > picks up a section label. But I think you can change the title > in section labels.

28.11.2 Pandoc

  • LaTeX encoding of tables is heavy (every cell is a minipage! > Specifies detailed widths)

  • Tables: no colspan nor rowspan yet

  • Indented blocks (statements, arguments, …) and AMS theorems

  • HTML default encoding of formulas uses unicode + italics + “math > inline” custom style class. Use --mathjax flag; adds a link to > mathjax.js in the head so this should be present on the website > (or unnecessary if the galley has its own head). See pandoc > manual on maths in > html > .

28.11.3 LaTeX

  • Standard logic symbols: \neg, \lnot, \land, \lor, \sim all well > supported in MathML? (Not a big worry!)