Multiple platform build/check report for BioC 3.22 - BUILD results for ontoProc on nebbiolo2

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"	4719
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4538
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4522
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4543
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: 2.3.9

Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 ontoProc

StartedAt: 2025-09-12 19:01:25 -0400 (Fri, 12 Sep 2025)

EndedAt: 2025-09-12 19:03:46 -0400 (Fri, 12 Sep 2025)

EllapsedTime: 141.2 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 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
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  zero-length arrow is of indeterminate angle and so skipped

Quitting from ontoProc.Rmd:121-125 [donew]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `py_call_impl()`:
! TypeError: 'http://purl.obolibrary.org/obo/STATO_0000416' belongs to more than one entity types (cannot be both a property and a class/an individual)!
Run `reticulate::py_last_error()` for details.
---
Backtrace:
    ▆
 1. └─ontoProc::quickOnto("cl.owl")
 2.   └─ontoProc::setup_entities2(targ)
 3.     └─basilisk::basiliskRun(...)
 4.       └─ontoProc (local) fun(...)
 5.         └─o2$get_ontology(owlfn)$load()
 6.           └─reticulate:::py_call_impl(callable, call_args$unnamed, call_args$named)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'ontoProc.Rmd' failed with diagnostics:
TypeError: 'http://purl.obolibrary.org/obo/STATO_0000416' belongs to more than one entity types (cannot be both a property and a class/an individual)!
Run `reticulate::py_last_error()` for details.
--- failed re-building ‘ontoProc.Rmd’

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

Quitting from owlents.Rmd:49-54 [lkcl]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `mat[, term_index]`:
! subscript out of bounds
---
Backtrace:
     ▆
  1. └─ontoProc::onto_plot2(cle, sel)
  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 'owlents.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘owlents.Rmd’

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

Error: Vignette re-building failed.
Execution halted