Multiple platform build/check report for BioC 3.21 - BUILD results for ontoProc on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4833
merida1	macOS 12.7.6 Monterey	x86_64	4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"	4614
kjohnson1	macOS 13.7.5 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4555
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4586
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 nebbiolo1

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: 2.2.4

Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data ontoProc

StartedAt: 2025-10-15 18:57:28 -0400 (Wed, 15 Oct 2025)

EndedAt: 2025-10-15 19:02:11 -0400 (Wed, 15 Oct 2025)

EllapsedTime: 282.3 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data 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
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  zero-length arrow is of indeterminate angle and so skipped
--- finished re-building ‘ontoProc.Rmd’

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

Quitting from owlents.Rmd:33-47 [getcl]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `py_call_impl()`:
! owlready2.base.OwlReadyOntologyParsingError: NTriples parsing error (or unrecognized file format) in /tmp/RtmpoyvPDM/file12ea2f5c45139b.
Run `reticulate::py_last_error()` for details.
---
Backtrace:
    ▆
 1. └─ontoProc::setup_entities(tf)
 2.   └─o2$get_ontology(owlfn)$load()
 3.     └─reticulate:::py_call_impl(callable, call_args$unnamed, call_args$named)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'owlents.Rmd' failed with diagnostics:
owlready2.base.OwlReadyOntologyParsingError: NTriples parsing error (or unrecognized file format) in /tmp/RtmpoyvPDM/file12ea2f5c45139b.
Run `reticulate::py_last_error()` for details.
--- failed re-building ‘owlents.Rmd’

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

Error: Vignette re-building failed.
Execution halted