[Bioc-devel] Subject: CEMiTool 1.37.0 build failure on nebbiolo2: rmarkdown 2.32 with Pandoc 2.7.3

[Pedro Russo]

Dear Bioconductor team,

I am the maintainer of CEMiTool. CEMiTool 1.37.0 (commit dffeb39) is
currently failing on the nebbiolo2 builder while creating the vignette
CEMiTool.Rmd.

The reported error is:

Error: processing vignette 'CEMiTool.Rmd' failed with diagnostics:
pandoc version 2.8 or higher is required and was not found
(see the help page ?rmarkdown::pandoc_available).

I was able to reproduce the failure locally using the same relevant
versions reported by the Bioconductor build environment.
Environment

Package: CEMiTool 1.37.0
Commit: dffeb39
R: 4.6.1
rmarkdown: 2.32
Pandoc: 2.7.3

The nebbiolo2 build information reports Pandoc 2.7.3, while the installed
rmarkdown version is 2.32.
Local reproduction

I used the Bioconductor Docker development image:

bioconductor/bioconductor_docker:devel

and installed rmarkdown 2.32 from the same repository used by the
Bioconductor environment:

https://p3m.dev/cran/__linux__/noble/latest/src/contrib

I then used Pandoc 2.7.3 and confirmed:

packageVersion("rmarkdown")# [1] "2.32"
rmarkdown::pandoc_version()# [1] "2.7.3"
rmarkdown::pandoc_available(version = "2.8")# [1] FALSE

Running:

R CMD build --keep-empty-dirs --no-resave-data --md5 .

produces:

* creating vignettes ... ERROR
--- re-building 'CEMiTool.Rmd' using rmarkdown
Error: processing vignette 'CEMiTool.Rmd' failed with diagnostics:
pandoc version 2.8 or higher is required and was not found
(see the help page ?rmarkdown::pandoc_available).
--- failed re-building 'CEMiTool.Rmd'

SUMMARY: processing the following file failed:
  'CEMiTool.Rmd'

Error: Vignette re-building failed.
Execution halted

Comparison

Using the same CEMiTool commit with the current Bioconductor Docker
environment, which has:

rmarkdown 2.31
Pandoc 3.10.2

the package builds successfully:

* creating vignettes ... OK
* building 'CEMiTool_1.37.0.tar.gz'

I also ran:

R CMD check --no-manual CEMiTool_1.37.0.tar.gz

which completed with:

Status: 1 NOTE

and no ERRORs or WARNINGs. The NOTE consists of standard R static-analysis
messages regarding visible bindings/global functions.
Conclusion

"The failure appears to be reproducible when rmarkdown 2.32 is used with
Pandoc 2.7.3. Could you please confirm whether this is expected for the
current nebbiolo2 build environment, and whether the builder can be updated
to Pandoc >= 2.8?

Since rmarkdown 2.32 requires Pandoc >= 2.8 for the vignette processing in
question, could the nebbiolo2 builder be updated to use Pandoc >= 2.8 (or
otherwise avoid this incompatible combination)?

Thank you.

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