pandoc `> 3.8` gives error for Markdown Table Cell Notebook Export to PDF and `nbconvert` ( but pandoc `< 3.8.1` works fine)

[fortunewalla]

Tried different Google solutions & also updated texlive, latex-recommended, nbconvert, etc... but only downgrading pandoc to 3.8 worked.

The markdown table code in a jupyter notebook cell marked as markdown

| Header 1 | Header 2 | Header 3 |
| -- | -- | -- |
| Row 1 Col 1 | Row 1 Col 2 | Row 1 Col 3 |
| Row 2 Col 1 | Row 2 Col 2 | Row 2 Col 3 |

Jupyter versions

$ jupyter --version
Selected Jupyter core packages...
IPython          : 8.37.0
ipykernel        : 7.1.0
ipywidgets       : 8.1.8
jupyter_client   : 8.6.3
jupyter_core     : 5.9.1
jupyter_server   : 2.17.0
jupyterlab       : 4.4.10
nbclient         : 0.10.2
nbconvert        : 7.16.6
nbformat         : 5.10.4
notebook         : 7.4.7
qtconsole        : 5.7.0
traitlets        : 5.14.3

Installing with mamba install pandoc

$ pandoc --version
pandoc 3.8.2.1
Features: +server +lua
Scripting engine: Lua 5.4
User data directory: /home/linux/.local/share/pandoc

Using pandoc ver 3.8.2.1 with Notebook --> Export to PDF

[I 2025-11-05 03:56:17.768 ServerApp] Saving file at /jpy.ipynb
[I 2025-11-05 03:56:24.303 ServerApp] Writing 21158 bytes to notebook.tex
[I 2025-11-05 03:56:24.319 ServerApp] Building PDF
[I 2025-11-05 03:56:24.338 ServerApp] Running xelatex 3 times: ['xelatex', 'notebook.tex', '-quiet']
[C 2025-11-05 03:56:28.978 ServerApp] xelatex failed: ['xelatex', 'notebook.tex', '-quiet']
    b"This is XeTeX, Version 3.141592653-2.6-0.999995 (TeX Live 2023/Debian) (preloaded format=xelatex)\n restricted \\write18 enabled.\nentering extended mode\n(./notebook.tex\nLaTeX2e <2023-11-01> patch level 1\nL3 programming layer <2024-01-22>\n(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls\nDocument Class: article 2023/05/17 v1.4n Standard LaTeX document 

.....
......
......


* (1in=72.27pt=25.4mm, 1cm=28.453pt)


    Package hyperref Warning: Rerun to get /PageLabels entry.

    (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd)
    (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd)
    (/usr/share/texlive/texmf-dist/tex/latex/jknapltx/ursfs.fd)

    LaTeX Warning: No \author given.


    LaTeX Font Warning: Font shape `U/rsfs/m/n' in size <5.475> not available
    (Font)              size <5> substituted on input line 416.


    ! LaTeX Error: No counter 'none' defined.

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

    l.433 \begin{longtable}[]{@{}lll@{}}

    ?
    ! Emergency stop.
     ...

    l.433 \begin{longtable}[]{@{}lll@{}}

    No pages of output.
    Transcript written on notebook.log.

Using pandoc ver 3.8.2.1 with nbconvert CLI

$ jupyter nbconvert jpy.ipynb --to pdf
[NbConvertApp] Converting notebook ujutest.ipynb to pdf
[NbConvertApp] Writing 21158 bytes to notebook.tex
[NbConvertApp] Building PDF
[NbConvertApp] Running xelatex 3 times: ['xelatex', 'notebook.tex', '-quiet']
[NbConvertApp] CRITICAL | xelatex failed: ['xelatex', 'notebook.tex', '-quiet']
b"This is XeTeX, Version 3.141592653-2.6-0.999995 (TeX Live 2023/Debian) (preloaded format=xelatex)\n restricted \\write18 enabled.\nentering extended mode\n(./notebook.tex\nLaTeX2e <2023-11-01> patch level 1\nL3 programming layer <2024-01-22>\n(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls\nDocument Class: article 2023/05/17 v1.4n Standard LaTeX document class

....
....
....

* (1in=72.27pt=25.4mm, 1cm=28.453pt)


Package hyperref Warning: Rerun to get /PageLabels entry.

(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd)
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd)
(/usr/share/texlive/texmf-dist/tex/latex/jknapltx/ursfs.fd)

LaTeX Warning: No \author given.


LaTeX Font Warning: Font shape `U/rsfs/m/n' in size <5.475> not available
(Font)              size <5> substituted on input line 416.


! LaTeX Error: No counter 'none' defined.

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

l.433 \begin{longtable}[]{@{}lll@{}}

?
! Emergency stop.
 ...

l.433 \begin{longtable}[]{@{}lll@{}}

No pages of output.
Transcript written on notebook.log.

Downgrading from 3.8.2.1 to 3.8

$ mamba install "pandoc<3.8.1"
conda-forge/linux-64                                        Using cache
conda-forge/noarch                                          Using cache

Pinned packages:

  - python=3.10


Transaction

  Prefix: /home/linux/miniforge3/envs/jup

  Updating specs:

   - pandoc<3.8.1


  Package   Version  Build       Channel           Size
─────────────────────────────────────────────────────────
  Downgrade:
─────────────────────────────────────────────────────────

  - pandoc  3.8.2.1  ha770c72_0  conda-forge     Cached
  + pandoc      3.8  ha770c72_0  conda-forge     Cached

  Summary:

  Downgrade: 1 packages

  Total download: 0 B

─────────────────────────────────────────────────────────


Confirm changes: [Y/n]

Transaction starting
Unlinking pandoc-3.8.2.1-ha770c72_0
Linking pandoc-3.8-ha770c72_0

Transaction finished

After Downgrading to pandoc ver 3.8 , nbconvert

$ jupyter nbconvert jpy.ipynb --to pdf
[NbConvertApp] Converting notebook jpy.ipynb to pdf
[NbConvertApp] Writing 20470 bytes to notebook.tex
[NbConvertApp] Building PDF
[NbConvertApp] Running xelatex 3 times: ['xelatex', 'notebook.tex', '-quiet']
[NbConvertApp] Running bibtex 1 time: ['bibtex', 'notebook']
[NbConvertApp] WARNING | bibtex had problems, most likely because there were no citations
[NbConvertApp] PDF successfully created
[NbConvertApp] Writing 7938 bytes to jpy.pdf
$ xpdf jpy.pdf

After Downgrading to pandoc ver 3.8, Jupyter Notebook Export to PDF

[W 2025-11-05 12:55:01.484 ServerApp] The websocket_ping_timeout (90000) cannot be longer than the websocket_ping_interval (30000).
    Setting websocket_ping_timeout=30000
[I 2025-11-05 12:55:01.491 ServerApp] Connecting to kernel 575f157b-9e99-4e55-a3f5-ee4365b1aeb6.
[I 2025-11-05 12:55:01.497 ServerApp] Connecting to kernel 575f157b-9e99-4e55-a3f5-ee4365b1aeb6.
[I 2025-11-05 12:55:07.828 ServerApp] Writing 20470 bytes to notebook.tex
[I 2025-11-05 12:55:07.828 ServerApp] Building PDF
[I 2025-11-05 12:55:07.828 ServerApp] Running xelatex 3 times: ['xelatex', 'notebook.tex', '-quiet']
[I 2025-11-05 12:55:11.851 ServerApp] Running bibtex 1 time: ['bibtex', 'notebook']
[W 2025-11-05 12:55:11.862 ServerApp] bibtex had problems, most likely because there were no citations
[I 2025-11-05 12:55:11.862 ServerApp] PDF successfully created

[fortunewalla]

This is the AI answer (not sure how accurate it is)

This appears to be caused by a change in Pandoc versions after 3.8 that requires longtable.sty version 4.21 or newer, while many systems ship with an older version.

Pandoc 3.8.2+ uses \LTcaptype in its table counter implementation which is only available in longtable package version 4.21 or newer. Standard Linux distributions (including Ubuntu) ship with older TeX Live versions containing longtable 1.04d (from TeX Live 2023). Without \LTcaptype, LaTeX cannot properly handle the new counter mechanism.

[ojk-07]

I have the same problem in my miniconda environment on Windows 11. After downgrading Pandoc to 3.8.0, the problem doesn't occur anymore.
I analysed it and also opened an issue describing the logtable problem in a bit more detail.