pandoc-crossref will fail if these commented out

[sunt05]

Just discovered your great work!
HUGE THANKS!!!

One issue identified if using pandoc with pandoc-crossref:

rticles/inst/rmarkdown/templates/copernicus_article/resources/template.tex

Lines 84 to 86 in 3445b46

	%$for(header-includes)$
	%$header-includes$
	%$endfor$

If these lines are commented out, then the headers by pandoc-crossref won't be correctly inserted.

[yihui]

There is a comment on the previous line:

rticles/inst/rmarkdown/templates/copernicus_article/resources/template.tex

Lines 83 to 86 in 3445b46

	% The "Technical instructions for LaTex" by Copernicus require _not_ to insert any additional packages.
	%$for(header-includes)$
	%$header-includes$
	%$endfor$

Cc the template author @nuest (#172). I'm not the expert here.

[nuest]

Copernicus discourages adding any additional packages, see https://publications.copernicus.org/for_authors/manuscript_preparation.html

IIRC correctly that is why is disabled that option for authors, however, I was not aware that the pandoc-crossref filter would be impacted by that.

@sunt05 Can you please provide a reproducible example so I can take a closer look? Thanks!

[cderv]

@sunt05 friendly ping here 😄
Can you provide a reproducible example for @nuest ?

[sunt05]

Thanks @cderv for the reminder! 😅
Sorry about the delay: as it's been a while since I tested the templated, I needed a bit longer to re-pick this up.

Now please test the template with files in this repo:
https://github.com/sunt05/test-r-template

issue

if the above mentioned lines are commented out as instructed by Copernicus, the following issue would appear:

Error producing PDF.
! You can't use `\spacefactor' in vertical mode.
\@->\spacefactor 
                 \@m {}
l.77 \@

[cderv]

It seems you are not using rticles and rmarkdown R 📦 to render your document. Is it just for the example or are you always using template this way ?

I believe the tex template are best used with those 2 packages package: rmarkdown::render() function and rticles::copernicus_article() format .

[sunt05]

It seems you are not using rticles and rmarkdown R 📦 to render your document. Is it just for the example or are you always using template this way ?

I'm always using it this way: i.e., with pandoc, as I found the templates could be easily adapted for broader applicability with more generic markdown-based tools, e.g., pandoc

I believe the tex template are best used with those 2 packages package: rmarkdown::render() function and rticles::copernicus_article() format .

Sorry that if this issue looks off-topic: please feel free to close it.

[cderv]

I'm always using it this way: i.e., with pandoc, as I found the templates could be easily adapted for broader applicability with more generic markdown-based tools, e.g., pandoc

You may already know but rmarkdown also use pandoc for conversion.

I believe the issue you get if from converting directly using the template. I did not identify why yet but I don't get the same tex file after pandoc conversion from the command line or using rmarkdown::render. That means some things is happening when using Rmarkdown that you need to reproduce using pandoc;

[sunt05]

I believe the issue you get if from converting directly using the template. I did not identify why yet but I don't get the same tex file after pandoc conversion from the command line ...

Did you use the following line to reproduce the error?

pandoc -f markdown+tex_math_single_backslash -o Manuscript.pdf --pdf-engine=pdflatex --template=template.tex --filter=pandoc-crossref test.md

Please note the template.tex file is a modified version, which can successfully produce a PDF.

I just update the repo with more description to reproduce the error as mentioned above:

pandoc -f markdown+tex_math_single_backslash -o Manuscript.pdf --pdf-engine=pdflatex --template=template_orig.tex --filter=pandoc-crossref test.md

Sorry about any confusion I might have brought up.

[cderv]

I can reproduce using your command. But I cannot reproduce if I use rmarkdown and rticles directly.
and I believe this comes from pandoc-crossref that you are using.

pandoc-crossref is doing some stuff with the header-includes part, see https://github.com/lierdakil/pandoc-crossref/blob/master/lib/Text/Pandoc/CrossRef/Util/ModifyMeta.hs

So I don't think it likes this template that have this part commented. This is a compatibility issue with pandoc-crossref I believe.

Best thing to do here is to use your own template I think

[sunt05]

Thanks for the discussion and help! @cderv

I'll use the templates more wisely with pandoc-crossref 😃

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