Multiple platform build/check report for BioC 3.21 - BUILD results for ontoProc on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences"	4742
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences"	4545
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4576
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4528
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4459
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 lconway

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: 2.1.7

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

StartedAt: 2025-03-18 17:53:45 -0400 (Tue, 18 Mar 2025)

EndedAt: 2025-03-18 18:03:44 -0400 (Tue, 18 Mar 2025)

EllapsedTime: 599.6 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ontoProc
###
##############################################################################
##############################################################################


* 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
2025-03-18 17:54:44.349 R[3454:436023721] XType: com.apple.fonts is not accessible.
2025-03-18 17:54:44.349 R[3454:436023721] XType: XTFontStaticRegistry is enabled.
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  zero-length arrow is of indeterminate angle and so skipped

Quitting from ontoProc.Rmd:121-124 [donew]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `mat[, term_index]`:
! subscript out of bounds
---
Backtrace:
     ▆
  1. └─ontoProc::onto_plot2(cl, gsub(":", "_", stab$tag))
  2.   └─ontologyPlot::onto_plot(ont, terms2use, ...)
  3.     ├─base::lapply(...)
  4.     │ └─ontologyPlot (local) FUN(X[[i]], ...)
  5.     │   └─(function() {...
  6.     └─ontologyPlot::remove_uninformative_terms(ontology, term_sets)
  7.       └─ontologyPlot:::remove_uninformative_once(...)
  8.         └─base::sapply(...)
  9.           └─base::lapply(X = X, FUN = FUN, ...)
 10.             └─ontologyPlot (local) FUN(X[[i]], ...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'ontoProc.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘ontoProc.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted