Biblatex related issue caused by Quarto update (probably due to Pandoc update from 3.1.13 to 3.2)

[juliantao]

Bug description

I use quarto to prepare my CV, I just reconfigured quarto based on the latest commit before rendering my CV. However, it throws errors complaining about missing files:

updating tlmgr

updating existing packages
finding package for numeric.dbx
finding package for biblatex-dm.cfg
finding package for JulianTaoCV.bbl
ERROR: 
compilation failed- no matching packages
Emergency stop.
<*> JulianTaoCV.tex
                    

see /home/julian/Dropbox (ASU)/jtaocv/JulianTaoCV.log for more information.
ERROR: Error
    at renderFiles (file:///home/julian/quarto-cli/src/command/render/render-files.ts:
350:23)
    at eventLoopTick (ext:core/01_core.js:153:7)
    at async renderProject (file:///home/julian/quarto-cli/src/command/render/project.
ts:440:23)
    at async renderForPreview (file:///home/julian/quarto-cli/src/command/preview/prev
iew.ts:428:24)
    at async render (file:///home/julian/quarto-cli/src/command/preview/preview.ts:172
:22)
    at async preview (file:///home/julian/quarto-cli/src/command/preview/preview.ts:18
9:18)
    at async Command.actionHandler (file:///home/julian/quarto-cli/src/command/preview
/cmd.ts:421:7)
    at async Command.execute (file:///home/julian/quarto-cli/src/vendor/deno.land/x/cl
iffy@v1.0.0-rc.3/command/command.ts:1948:7)
    at async Command.parseCommand (file:///home/julian/quarto-cli/src/vendor/deno.land
/x/cliffy@v1.0.0-rc.3/command/command.ts:1780:14)
    at async quarto (file:///home/julian/quarto-cli/src/quarto.ts:159:5)

I tried to reinstall TinyTex, cleanup other versions of textlive, updating packages using tlmgr, but none of them worked.

I later reconfigured quarto based on an earlier commit when pandoc 3.1.13 is still used, the rendering was successful and I was able to generate the PDF as before.

Thus, I suspect that the error was due to the update of Pandoc.

Steps to reproduce

1. Fork my CV repo, https://github.com/juliantao/jtaocv
2. It is suggested to use the virtual environment based on the renv.lock file. This makes sure that necessary packages are installed and the correct versions of two important packages RefManageR and bibtex are used
3. configure quarto based on the latest commit, by following the instructions here https://github.com/quarto-dev/quarto-cli

git clone https://github.com/quarto-dev/quarto-cli
cd quarto-cli
./configure.sh

4. Go to the CV folder, render any of the qmd files, such as the JulianTaoCV_1page. The above errors will appear, and the rendering will be terminated immaturely.
5. Use an earlier version of quarto, for example, 9557992, reconfigure quarto

cd quarto-cli
git checkout 95579925
./configure.sh

6. then go to the CV folder again, render the same qmd file. This should result in successful rendering.

Expected behavior

No response

Actual behavior

No response

Your environment

No response

Quarto check output

Quarto 99.9.9
[✓] Checking versions of quarto binary dependencies...
      Pandoc version 3.1.13: OK
      Dart Sass version 1.70.0: OK
      Deno version 1.41.0: OK
      Typst version 0.11.0: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
      Version: 99.9.9
fatal: not a git repository (or any of the parent directories): .git
      Path: /home/julian/quarto-cli/package/dist/bin

[✓] Checking tools....................OK
      TinyTeX: v2024.06
      Chromium: 869685

[✓] Checking LaTeX....................OK
      Using: TinyTex
      Path: /home/julian/.TinyTeX/bin/x86_64-linux
      Version: 2024

[✓] Checking basic markdown render....OK

[✓] Checking Python 3 installation....OK
      Version: 3.10.12
      Path: /usr/bin/python3
      Jupyter: 4.10.0
      Kernels: python3

(/) Checking Jupyter engine render....[IPKernelApp] ERROR | No such comm target registered: quarto_kernel_setup
[✓] Checking Jupyter engine render....OK

[✓] Checking R installation...........OK
      Version: 4.1.2
      Path: /usr/lib/R
      LibPaths:
        - /home/julian/R/x86_64-pc-linux-gnu-library/4.1
        - /usr/local/lib/R/site-library
        - /usr/lib/R/site-library
        - /usr/lib/R/library
      knitr: 1.43
      rmarkdown: 2.23

[✓] Checking Knitr engine render......OK

[mcanouil]

Could you provide all requested information and the command you ran?

Also what do you mean by "caused by updating Pandoc from 3.1.13 to 3.2"? Are you talking about the embedded version of Pandoc inside Quarto or a local version you have? Quarto should not use your system version of Pandoc, if it does it means your install is somehow corrupted.

Side note: do not use date: "`r format(Sys.Date(), '%B %Y')`" to set the date, see https://quarto.org/docs/reference/dates.html.

[mcanouil]

I can't run your repository because you are using old packages that require compilation.
Using latest packages seems to break your workflow but possibly solves the LaTeX issue if it only appears with this repository.

Additionally, you are using Pandoc options Rmarkdown syntax, etc.
I suggest:

• you drop the header-includes and use https://quarto.org/docs/output-formats/pdf-basics.html#output-options
• use raw markup syntax to include raw LaTeX, see https://quarto.org/docs/authoring/markdown-basics.html#raw-content.
• use YAML option syntax.
  Instead of ```{r awards, results='asis'} use:

  ```{r}
  #| label: awards
  #| results: asis
  ...

[juliantao]

Could you provide all requested information and the command you ran?

Also what do you mean by "caused by updating Pandoc from 3.1.13 to 3.2"? Are you talking about the embedded version of Pandoc inside Quarto or a local version you have? Quarto should not use your system version of Pandoc, if it does it means your install is somehow corrupted.

Side note: do not use date: "`r format(Sys.Date(), '%B %Y')`" to set the date, see https://quarto.org/docs/reference/dates.html.

Hi,
Thanks for the quick reply. I updated some info in the post, please check out.

I did not use my own Pandoc. I reconfigured quarto based on the git commits. Based on my description, I suspect that the error was due to a Pandoc update, which Quarto embraced.

[juliantao]

I can't run your repository because you are using old packages that require compilation. Using latest packages seems to break your workflow but possibly solves the LaTeX issue if it only appears with this repository.

Additionally, you are using Pandoc options Rmarkdown syntax, etc. I suggest:

• you drop the header-includes and use https://quarto.org/docs/output-formats/pdf-basics.html#output-options
• use raw markup syntax to include raw LaTeX, see https://quarto.org/docs/authoring/markdown-basics.html#raw-content.
• use YAML option syntax.
  Instead of ```{r awards, results='asis'} use:

  ```{r}
  #| label: awards
  #| results: asis
  ...

I did some customization on the bib fields. Did you use the virtual environment of the directory? I previously noticed that there were issues with newer versions of RefManageR and bibtex R packages.

Thanks for the other tips as well!

[mcanouil]

You have no virtual environment, you only have a renv setup.

Note that the error you get is a LaTeX error: JulianTaoCV_1page.bbl is not found by the LaTeX engine.
I suggest you investigate your tex file.
You can add keep-tex: true.

edit: you should look for a "bib" file probably something like: \addbibresource{***.bib} added by your code.

See that it compiles without your code, so the issue is somewhere there:

[juliantao]

Thanks, @mcanouil.
To provide you more background:

1. My quarto CV project is quite complex, but I have used it for quite some time, it works on my side using an older version of the Quarto, as shown from the history of the repo. I tried my best to make it reproducible.
2. I already spent several hours on this issue. I ruled out many factors and narrowed it down to Pandoc version.
3. Regarding the source bib file, I was using a .tex template (https://github.com/juliantao/jtaocv/tree/main/_extensions/cv) where customization of the bib fields as well as the inclusion of my bib file was achieved.
4. I checked the tex file and the corresponding log file, which did not give very useful information.
5. "JulianTaoCV_1page.bbl is not found by the LaTeX engine.": exactly, this means that the source of error is the biblatex, biber or bibtex, which failed to generate the expected bbl file.

[mcanouil]

My quarto CV project is quite complex,

Indeed, which makes it hard for us to use, so you have to remove pieces of your CV until you get something small that exhibits the issue.
You changed entirely the Pandoc template with yours, meaning you no longer account for any change for that.

For instance, you could try to use keep-md: true to get the result of your R code, without the actual R code. Then remove pieces of your markdown only document.

[juliantao]

Indeed, which makes it hard for us to use

I apologize for any inconvenience. I'm posting this here in the hope that it might help the developers identify a specific commit that caused an issue related to biblatex and/or pandoc. I understand this isn't the ideal way to report a problem.

I'll try to provide a minimal example, but it may take some time as I currently lack the bandwidth.

Thank you!

[mcanouil]

Ok, I did the debugging for you. Note that I basically remove piece by piece the content of your CV, nothing fancy, simply tedious as any debugging.
The issue is your "baretable" function.

If you set:

source("preprocess.R")
baretable <- function(tbl, ...) knitr::kable(tbl)

This should be in your template since you have a custom one or in include-before-body.

\titlespacing{\section}{0pt}{1.ex}{0.5ex}
\thispagestyle{empty}

[mcanouil]

A bit more detail, the issue is that the R code produces:

\begin{longtable}{lllll}
  \textbf{PhD}  & Civil Engineering & Case Western Reserve University & Cleveland, US & 2013 \\ 
  \textbf{MS}  & Civil Engineering & Tongji University & Shanghai, China & 2009 \\ 
  \textbf{BS}  & Civil Engineering & China University of Geosciences & Wuhan, China & 2006 \\ 
  \end{longtable}

See the bad indentation for the closing? That's the issue.

This is what "your" code is producing:

Here, the issue is:

print(xtable::xtable(head(mtcars)), hline.after = NULL, tabular.environment = "longtable", booktabs = TRUE)

% latex table generated in R 4.4.0 by xtable 1.8-4 package
% Thu Jun  6 22:36:04 2024
\begin{longtable}{rrrrrrrrrrrr}
  & mpg & cyl & disp & hp & drat & wt & qsec & vs & am & gear & carb \\ 
 Mazda RX4 & 21.00 & 6.00 & 160.00 & 110.00 & 3.90 & 2.62 & 16.46 & 0.00 & 1.00 & 4.00 & 4.00 \\ 
  Mazda RX4 Wag & 21.00 & 6.00 & 160.00 & 110.00 & 3.90 & 2.88 & 17.02 & 0.00 & 1.00 & 4.00 & 4.00 \\ 
  Datsun 710 & 22.80 & 4.00 & 108.00 & 93.00 & 3.85 & 2.32 & 18.61 & 1.00 & 1.00 & 4.00 & 1.00 \\ 
  Hornet 4 Drive & 21.40 & 6.00 & 258.00 & 110.00 & 3.08 & 3.21 & 19.44 & 1.00 & 0.00 & 3.00 & 1.00 \\ 
  Hornet Sportabout & 18.70 & 8.00 & 360.00 & 175.00 & 3.15 & 3.44 & 17.02 & 0.00 & 0.00 & 3.00 & 2.00 \\ 
  Valiant & 18.10 & 6.00 & 225.00 & 105.00 & 2.76 & 3.46 & 20.22 & 1.00 & 0.00 & 3.00 & 1.00 \\ 
  \end{longtable}
Warning message:
In print.xtable(xtable::xtable(head(mtcars)), hline.after = NULL,  :
  Attempt to use "longtable" with floating = TRUE. Changing to FALSE.

Setting booktabs = FALSE solves the indentation issue that LaTeX does not like.