Multiple platform build/check report for BioC 3.19 - BUILD results for autonomics on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"	4708
palomino3	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences"	4446
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"	4471
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences"	4426
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*

To the developers/maintainers of the autonomics package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/autonomics.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.

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data autonomics
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* checking for file ‘autonomics/DESCRIPTION’ ... OK
* preparing ‘autonomics’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘autonomics_detailed_manual.Rmd’ using rmarkdown

Quitting from lines 24-38 [unnamed-chunk-1] (autonomics_detailed_manual.Rmd)
Error: processing vignette 'autonomics_detailed_manual.Rmd' failed with diagnostics:
unused arguments (phosphofile = file.phosphosites, proteinfile = file.proteingroups)
--- failed re-building ‘autonomics_detailed_manual.Rmd’

--- re-building ‘autonomics_platformaware_analysis.Rmd’ using rmarkdown

Quitting from lines 51-54 [unnamed-chunk-2] (autonomics_platformaware_analysis.Rmd)
Error: processing vignette 'autonomics_platformaware_analysis.Rmd' failed with diagnostics:
object 'sep' not found
--- failed re-building ‘autonomics_platformaware_analysis.Rmd’

--- re-building ‘autonomics_unified_modeling.Rmd’ using rmarkdown

Quitting from lines 57-62 [unnamed-chunk-4] (autonomics_unified_modeling.Rmd)
Error: processing vignette 'autonomics_unified_modeling.Rmd' failed with diagnostics:
object 'sep' not found
--- failed re-building ‘autonomics_unified_modeling.Rmd’

SUMMARY: processing the following files failed:
  ‘autonomics_detailed_manual.Rmd’
  ‘autonomics_platformaware_analysis.Rmd’
  ‘autonomics_unified_modeling.Rmd’

Error: Vignette re-building failed.
Execution halted

BUILD results for autonomics on lconway

Summary

Command output