Fix counter needed in pandoc 3.8.2 and later#116
Open
zeehio wants to merge 2 commits into
Open
Conversation
zeehio
changed the title
zeehio
force-pushed
the
fix-pandoc-382-counter
branch
from
July 11, 2026 06:30
1db6d0d to
5e905a4
Compare
pandoc<3.8.1 works pandoc==3.8.1 does not work pandoc>=3.8.2 works 3.8.2 was released one week after 3.8.1 See jgm/pandoc#11201 and rstudio/rticles#595
zeehio
force-pushed
the
fix-pandoc-382-counter
branch
from
July 11, 2026 06:31
5e905a4 to
8478c44
Compare
zeehio
pushed a commit
to sipss/AlpsNMR
that referenced
this pull request
Jul 11, 2026
…ignette failure
pandoc >=3.8.1 emits \LTcaptype{none} for uncaptioned longtables, and
stock BiocStyle's LaTeX template never predefines a counter named
"none", causing "LaTeX Error: No counter 'none' defined" when
building vignettes (this is what's been failing check-bioc.yml).
Confirmed via a minimal reprex against official BiocStyle 2.40.0 with
pandoc 3.1.3 (works) vs 3.8.2.1 (fails, same error).
Installs the fork right after dependency-installation pass 1 and
before pass 2 (the step that actually builds vignettes via
remotes::install_local(build_vignettes = TRUE)). The fork's
Version: 2.41.0 outranks the official release's 2.40.0, so pass 2's
own upgrade = TRUE won't revert it.
Temporary until Bioconductor/BiocStyle#116
lands upstream.
4 tasks
…onductor#116) Renders the pipe-table reprex from Bioconductor#116 through BiocStyle::pdf_document with lualatex. Without the fix in inst/rmd/latex/default-2.8.tex, compilation fails with "! LaTeX Error: No counter '' defined." on pandoc >=3.8.1 (jgm/pandoc#11201).
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
BiocStyle::pdf_document fails on recent pandoc versions. Since pandoc 3.8.2, pandoc requires the latex template to include a counter definition that BiocStyle is missing.
I have tested this fix with pandoc 3.1.3 (worked before and after the fix), pandoc 3.8.1 (does not work, it is a botched release superseded one week after by 3.8.2) pandoc 3.8.2 (needs this fix) and pandoc 3.10 (needs this fix).
See jgm/pandoc#11201 for the underlying issue and rstudio/rticles#595 for how it has been patched elsewhere.