Example not build

[natir]

Hello,

First thank for your work.

I try to use this project but when I try to run project on example make failled:

➜ make ARTICLE=example/paper.md
INARA_ARTIFACTS_PATH=publishing-artifacts/ pandoc \
  --data-dir=data \
  --defaults=shared \
  --defaults=pdf.yaml \
  --defaults=resources/joss/defaults.yaml \
  --resource-path=.:resources:example/ \
  --metadata=article-info-file=resources/default-article-info.yaml \
  --variable=joss \
  --output=publishing-artifacts/paper.pdf \
  example/paper.md
[INFO] Running filter data/filters/parse-latex.lua
[INFO] Completed filter data/filters/parse-latex.lua in 2 ms
[INFO] Running filter data/filters/inline-cited-references.lua
Error running filter data/filters/inline-cited-references.lua:
data/filters/inline-cited-references.lua:6: attempt to call a nil value (field 'references')
stack traceback:
	data/filters/inline-cited-references.lua:6: in function 'Pandoc'
make: *** [Makefile:33 : publishing-artifacts/paper.pdf] Erreur 83
```

System:
- Fedora: 36
- pandoc: 2.14
- make: 4.3
- lua 5.4.4
- pdfTeX: 3.141592653-2.6-1.40.22
- TeX Live 2021 full install

[tarleb]

Thanks for reporting this. It looks like we expect the paper to have at least one entry in the bibliography, but that's not a good assumption to make and should be fixed.

[natir]

I add citation and autoreference in example document and I still get same error.

diff --git a/example/paper.md b/example/paper.md
index 7dcd5fb..6eef7df 100644
--- a/example/paper.md
+++ b/example/paper.md
@@ -157,6 +157,8 @@ the [pandoc manual](https://pandoc.org/MANUAL#extension-citations)
 for additional features, including page locators, prefixes,
 suffixes, and suppression of author names in citations.

+test @smith2018 [@bradford197]
+
 ### Mathematical Formulæ

 Equations and other math content has is marked by dollar signs (`$`). A
@@ -404,6 +406,8 @@ number of the referenced float. E.g., in this document
 | Lua      | dynamic, strong | yes               | strict     | 1993    |
 | C        | static, weak    | no                | strict     | 1972    |

+Ref to table \autref{proglangs} \ref{proglangs}
+
 ## Equations

 Cross-references to equations work similar to those for floating

[zyzzyxdonta]

I ran into this same issue. This even happens with the example paper.

Pandoc version is:

pandoc 2.14.0.3
Compiled with pandoc-types 1.22.1, texmath 0.12.3.3, skylighting 0.10.5.2,
citeproc 0.4.0.1, ipynb 0.1.0.1

Please let me know if you need any further information.

[tarleb]

Thank you. Does this still happen with pandoc 3.1?

[zyzzyxdonta]

Thank you for the quick response. I wasn't aware my OS didn't ship the newest version. So I tried with the newest binary from GitHub:

pandoc 3.1.2
Features: +server +lua
Scripting engine: Lua 5.4
User data directory: /home/x/.local/share/pandoc
Copyright (C) 2006-2023 John MacFarlane. Web:  https://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.

This seems to solve the initial problem. However, I now run into another error:

INARA_ARTIFACTS_PATH=publishing-artifacts/ /home/x/Downloads/pandoc-3.1.2/bin/pandoc \
  --data-dir=data \
  --defaults=shared \
  --defaults=pdf.yaml \
  --defaults=resources/joss/defaults.yaml \
  --resource-path=.:resources:./ \
  --metadata=article-info-file=resources/default-article-info.yaml \
  --variable=joss \
  --output=publishing-artifacts/paper.pdf \
  paper.md
[INFO] Running filter data/filters/parse-latex.lua
[INFO] Completed filter data/filters/parse-latex.lua in 7 ms
[INFO] Running filter data/filters/inline-cited-references.lua
[INFO] Loaded paper.bib from paper.bib
[INFO] Completed filter data/filters/inline-cited-references.lua in 22 ms
[INFO] Running filter citeproc
[INFO] Loaded apa.csl from resources/apa.csl
[INFO] Completed filter citeproc in 72 ms
[INFO] Running filter data/filters/normalize-metadata.lua
[INFO] Completed filter data/filters/normalize-metadata.lua in 9 ms
[INFO] Running filter data/filters/time.lua
[INFO] Completed filter data/filters/time.lua in 4 ms
[INFO] Running filter data/filters/normalize-author-names.lua
[INFO] Completed filter data/filters/normalize-author-names.lua in 24 ms
[INFO] Running filter data/filters/substitute-in-format.lua
[INFO] Completed filter data/filters/substitute-in-format.lua in 4 ms
[INFO] Running filter data/filters/add-images.lua
[INFO] Loaded joss/aas-logo.png from resources/joss/aas-logo.png
[INFO] Loaded joss/europar-logo.png from resources/joss/europar-logo.png
[INFO] Loaded joss/logo.png from resources/joss/logo.png
[INFO] Completed filter data/filters/add-images.lua in 5 ms
[INFO] Running filter data/filters/draft.lua
[INFO] Completed filter data/filters/draft.lua in 4 ms
[INFO] Running filter data/filters/self-citation.lua
JSON parse error: Error in $: Incompatible API versions: encoded with [1,23] but attempted to decode with [1,22,1].
Error running filter data/filters/self-citation.lua:
Error running filter pandoc:
Filter returned error status 64
stack traceback:
        data/filters/self-citation.lua:56: in function 'Meta'

[zyzzyxdonta]

I think this was due to the fact that you can only pass the Pandoc executable to make and the old pandoc-lua exe was used. After adding the downloaded files to the path, this error is gone, too. Thank you!

[tarleb]

Great to hear! I'll leave this open until we have more meaningful error messages.