Breakage caused by Pandoc 3.0.1

[yihui]

I received an email from CRAN notifying me of breakage of several packages caused by Pandoc 3.0.1. It seems Pandoc 3.0.1 is having trouble with certain .bib files. A few examples:

GREMLINS

Problem: https://www.stats.ox.ac.uk/pub/bdr/M1mac/GREMLINS.out

https://github.com/GrossSBM/GREMLINS/blob/3fb0d3f213bae9c729a47b9437791ab2f6c14697/vignettes/biblio.bib#L97

ANOVAreplication

Problem: https://www.stats.ox.ac.uk/pub/bdr/M1mac/ANOVAreplication.out

I don't know what's wrong with this bib file: https://github.com/cran/ANOVAreplication/blob/master/vignettes/Library_Marielle.bib

Full list

package	source	problem
ANOVAreplication	cran/ANOVAreplication	https://www.stats.ox.ac.uk/pub/bdr/M1mac/ANOVAreplication.out
GREMLINS	cran/GREMLINS	https://www.stats.ox.ac.uk/pub/bdr/M1mac/GREMLINS.out
MLML2R	cran/MLML2R	https://www.stats.ox.ac.uk/pub/bdr/M1mac/MLML2R.out
MODIStsp	cran/MODIStsp	https://www.stats.ox.ac.uk/pub/bdr/M1mac/MODIStsp.out
MTA	cran/MTA	https://www.stats.ox.ac.uk/pub/bdr/M1mac/MTA.out
MatchIt	cran/MatchIt	https://www.stats.ox.ac.uk/pub/bdr/M1mac/MatchIt.out
RGCCA	cran/RGCCA	https://www.stats.ox.ac.uk/pub/bdr/M1mac/RGCCA.out
RGENERATEPREC	cran/RGENERATEPREC	https://www.stats.ox.ac.uk/pub/bdr/M1mac/RGENERATEPREC.out
RNeXML	cran/RNeXML	https://www.stats.ox.ac.uk/pub/bdr/M1mac/RNeXML.out
SourceSet	cran/SourceSet	https://www.stats.ox.ac.uk/pub/bdr/M1mac/SourceSet.out
TOSTER	cran/TOSTER	https://www.stats.ox.ac.uk/pub/bdr/M1mac/TOSTER.out
TreeSearch	cran/TreeSearch	https://www.stats.ox.ac.uk/pub/bdr/M1mac/TreeSearch.out
TrenchR	cran/TrenchR	https://www.stats.ox.ac.uk/pub/bdr/M1mac/TrenchR.out
bootf2	cran/bootf2	https://www.stats.ox.ac.uk/pub/bdr/M1mac/bootf2.out
breathtestcore	cran/breathtestcore	https://www.stats.ox.ac.uk/pub/bdr/M1mac/breathtestcore.out
codyn	cran/codyn	https://www.stats.ox.ac.uk/pub/bdr/M1mac/codyn.out
colorSpec	cran/colorSpec	https://www.stats.ox.ac.uk/pub/bdr/M1mac/colorSpec.out
colorspace	cran/colorspace	https://www.stats.ox.ac.uk/pub/bdr/M1mac/colorspace.out
cricketdata	cran/cricketdata	https://www.stats.ox.ac.uk/pub/bdr/M1mac/cricketdata.out
dogesr	cran/dogesr	https://www.stats.ox.ac.uk/pub/bdr/M1mac/dogesr.out
indicspecies	cran/indicspecies	https://www.stats.ox.ac.uk/pub/bdr/M1mac/indicspecies.out
itp	cran/itp	https://www.stats.ox.ac.uk/pub/bdr/M1mac/itp.out
lifecontingencies	cran/lifecontingencies	https://www.stats.ox.ac.uk/pub/bdr/M1mac/lifecontingencies.out
mable	cran/mable	https://www.stats.ox.ac.uk/pub/bdr/M1mac/mable.out
prevtoinc	cran/prevtoinc	https://www.stats.ox.ac.uk/pub/bdr/M1mac/prevtoinc.out
sylly	cran/sylly	https://www.stats.ox.ac.uk/pub/bdr/M1mac/sylly.out
vegclust	cran/vegclust	https://www.stats.ox.ac.uk/pub/bdr/M1mac/vegclust.out

Warnings

package	source	problem
MorphoTools2	cran/MorphoTools2	https://www.stats.ox.ac.uk/pub/bdr/M1mac/MorphoTools2.out
RFmerge	cran/RFmerge	https://www.stats.ox.ac.uk/pub/bdr/M1mac/RFmerge.out
VARMER	cran/VARMER	https://www.stats.ox.ac.uk/pub/bdr/M1mac/VARMER.out
VedicDateTime	cran/VedicDateTime	https://www.stats.ox.ac.uk/pub/bdr/M1mac/VedicDateTime.out

[cderv]

Related issue on Ubuntu in rticles so I don't think this is M1 or fedora only. They may have updated pandoc there only 🤔

See rstudio/rticles#516 - it could be a good way to look into that;

[yihui]

I've finally finished examining all packages above. The main problem has been fixed in pandoc nightly: jgm/pandoc#8604

For packages in the "Warnings" section above, the problems were caused by raw tex code and HTML tags in title/date fields in YAML. I've sent PRs to packages that can be found on Github:

• Protect raw tex code for Pandoc 3.x MarekSlenker/MorphoTools2#3
• Remove the unnecessary <center> tags hzambran/RFmerge#9
• Remove the <h1> tag in subtitle prajwalkpatil/VedicDateTime#10

[cderv]

Awesome ! Thank you @yihui. I missed this Pandoc issue and fix. Hopefully they'll make a release.

[yihui]

They have released Pandoc 3.1: https://github.com/jgm/pandoc/releases/tag/3.1

[yihui]

All bibliography errors are gone. I have emailed the maintainers of the four packages in the Warnings section, so there is nothing left for us to do now.

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