Multiple platform build/check report for BioC 3.22 - BUILD results for cogeqc on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"	4901
lconway	macOS 12.7.6 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4691
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4637
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 cogeqc on kjohnson3

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

Version: 1.13.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data cogeqc

StartedAt: 2025-10-28 16:00:01 -0400 (Tue, 28 Oct 2025)

EndedAt: 2025-10-28 16:00:37 -0400 (Tue, 28 Oct 2025)

EllapsedTime: 35.4 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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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 cogeqc
###
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* checking for file ‘cogeqc/DESCRIPTION’ ... OK
* preparing ‘cogeqc’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘vignette_01_assessing_genome_assembly.Rmd’ using rmarkdown
2025-10-28 16:00:11.300 R[63343:567969657] XType: Using static font registry.
--- finished re-building ‘vignette_01_assessing_genome_assembly.Rmd’

--- re-building ‘vignette_02_assessing_orthogroup_inference.Rmd’ using rmarkdown

Quitting from vignette_02_assessing_orthogroup_inference.Rmd:236-239 [plot_species_tree]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `adjust_hclust_tip.edge.len()`:
! could not find function "adjust_hclust_tip.edge.len"
---
Backtrace:
    ▆
 1. └─cogeqc::plot_species_tree(tree)
 2.   └─ggtree::ggtree(tree)
 3.     ├─base::suppressWarnings(...)
 4.     │ └─base::withCallingHandlers(...)
 5.     ├─ggplot2::ggplot(...)
 6.     └─ggplot2:::ggplot.default(...)
 7.       ├─ggplot2::fortify(data, ...)
 8.       └─ggtree:::fortify.phylo(data, ...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'vignette_02_assessing_orthogroup_inference.Rmd' failed with diagnostics:
could not find function "adjust_hclust_tip.edge.len"
--- failed re-building ‘vignette_02_assessing_orthogroup_inference.Rmd’

--- re-building ‘vignette_03_assessing_synteny.Rmd’ using rmarkdown
--- finished re-building ‘vignette_03_assessing_synteny.Rmd’

SUMMARY: processing the following file failed:
  ‘vignette_02_assessing_orthogroup_inference.Rmd’

Error: Vignette re-building failed.
Execution halted