References are not beeing rendered anymore.

[m4x74]

Description

References of my thesis project are not being rendered correctly anymore. This only applies to the citations in the text body, the reference section at the end of the document is rendered fine. So the .bib file seems to be working.

When rendering, xelatex runs multiple loops, aborting after reaching the maximum number of runs. I found an old GitHub Issue from the Quarto Repository, suggesting that this might have something to do with LaTex packages not working correctly (see here https://github.com/quarto-dev/quarto-cli/issues/3518#issue-1469404408.

This also happens with previous version of my project, of which I'm sure, that they were working before. I assume that this is related to the new Quarto version 1.4, since this is the only thing I can think of that has changed since then. However, when not working with this project, e.g. basic Quarto scripts with pdf Output, references work fine.

I tried reproducing the error with the example of this repository, but here I got a different error:

ERROR: 
compilation failed- missing packages (automatic installed disabled)      
LaTeX Error: Something's wrong--perhaps a missing \item.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...

l.872 \end{CSLReferences}

Is anyone else having this problem?

[m4x74]

Short follow-up: It definitely seems to be an issue with the new quarto version. I was able to render the same project on a machine that uses Quarto 1.3.353. The machine unable to render the project runs Quarto 1.4.550.

[eeholmes-uw]

FYI this bug (not related but need to keep the note) https://github.com/quarto-dev/quarto-cli/issues/6867

[eeholmes-uw]

Ok, it still works under 1.4.433

Can you test with a small reprex? Like this to see if it is purely with the latest Quarto and shows up in simple examples?

---
title: "This is the title"
author: "Author One"
documentclass: book
link-citations: true
colorlinks: true
toc: true
numbersections: true
bibliography: [refer.bib]
---

# chapter

## section

**knitr** [@Xie2015] is a general-purpose package for dynamic report generation in R.

# references {.unnumbered}

::: {#refs}
:::

\appendix

# appendix

Hello

refer.bib

@Book{Xie2015,
  title = {Dynamic Documents with {R} and knitr},
  author = {Yihui Xie},
  publisher = {Chapman and Hall/CRC},
  address = {Boca Raton, Florida},
  year = {2015},
  edition = {2nd},
  note = {ISBN 978-1498716963},
  url = {https://yihui.org/knitr/},
}

[m4x74]

Your example works fine, for both HTML and PDF. Also, more comprehensive projects work fine. It seems to be related to the quarto-thesis-pdf class since the same project renders as an HTML.

[karamehmetfatih]

I encountered a similar problem with Quarto 1.4.554. Despite no alterations to my document, the crosslinking between citations and the references list isn't working. Upon inspecting the crosslink keys in the LaTeX document, I confirmed they match. While the reference list appears in the PDF, the in-text citations aren't linking to the references. I'd appreciate any insights on how you resolved this issue.

[karamehmetfatih]

I noticed that the biblatex bcf format version in the index-blx.bib file has changed from v3.10 to v3.11, and the biblatex-control argument also appears to have been modified. This change might be causing issues with rendering the PDF references.

Old Version

@Control{biblatex-control,
  options = {3.10:0:0:1:0:1:1:0:0:1:0:2:3:1:3:1:0:0:3:1:79:+:+:nyt},
}

New Version

@Control{biblatex-control,
  options = {3.11:0:0:1:0:1:1:0:0:1:0:2:3:1:3:1:0:0:3:1:79:+:+:nyt},
}

Could you please advise on how to resolve this issue?

[karamehmetfatih]

I was able to resolve the issue by downgrading Quarto from v1.5.57 to v1.3.450. It seems there may be a bug in the newer version of Quarto.

[m4x74]

Same experience! Still couldn't figure out what it is. This template still works: https://github.com/quarto-monash/thesis

[acebulsk]

I am also having the same issue. Steps to reproduce:

1. quarto use template nmfs-opensci/quarto-thesis
2. cd phd-thesis/
3. quarto render

Returns error:

ERROR: 
compilation failed- no matching packages
LaTeX Error: Something's wrong--perhaps a missing \item.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ... 
                                                  
l.872 \end{CSLReferences}

The relevant part of the log file says:

Package biblatex Info: Trying to load bibliographic data...
Package biblatex Info: ... file 'index.bbl' not found.
No file index.bbl.

Quarto Version: 1.4.533