Build/check report for BioC 3.20 - BUILD results for ontoProc on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4711
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

BUILD results for ontoProc on nebbiolo2

To the developers/maintainers of the ontoProc package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ontoProc.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: ontoProc

Version: 1.27.4

Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 ontoProc

StartedAt: 2024-09-06 18:38:12 -0400 (Fri, 06 Sep 2024)

EndedAt: 2024-09-06 18:43:18 -0400 (Fri, 06 Sep 2024)

EllapsedTime: 306.7 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 ontoProc
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* checking for file ‘ontoProc/DESCRIPTION’ ... OK
* preparing ‘ontoProc’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘ontoProc.Rmd’ using rmarkdown
Error running filter pandoc-citeproc:
Could not find executable pandoc-citeproc
Error: processing vignette 'ontoProc.Rmd' failed with diagnostics:
pandoc document conversion failed with error 83
--- failed re-building ‘ontoProc.Rmd’

--- re-building ‘owlents.Rmd’ using rmarkdown
Requirement already satisfied: owlready2 in /home/biocbuild/.virtualenvs/r-owlready2/lib/python3.10/site-packages (0.46)

[notice] A new release of pip is available: 24.1.2 -> 24.2
[notice] To update, run: /home/biocbuild/.virtualenvs/r-owlready2/bin/python -m pip install --upgrade pip
* Owlready2 * Warning: ignoring cyclic subclass of/subproperty of, involving:
  http://purl.obolibrary.org/obo/CHEBI_36080
  http://purl.obolibrary.org/obo/PR_000000001

Requirement already satisfied: owlready2 in /home/biocbuild/.virtualenvs/r-owlready2/lib/python3.10/site-packages (0.46)

[notice] A new release of pip is available: 24.1.2 -> 24.2
[notice] To update, run: /home/biocbuild/.virtualenvs/r-owlready2/bin/python -m pip install --upgrade pip
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  zero-length arrow is of indeterminate angle and so skipped
Error running filter pandoc-citeproc:
Could not find executable pandoc-citeproc
Error: processing vignette 'owlents.Rmd' failed with diagnostics:
pandoc document conversion failed with error 83
--- failed re-building ‘owlents.Rmd’

SUMMARY: processing the following files failed:
  ‘ontoProc.Rmd’ ‘owlents.Rmd’

Error: Vignette re-building failed.
Execution halted