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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 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
2025-10-05 18:16:55.972 R[60761:459244659] XType: com.apple.fonts is not accessible.
2025-10-05 18:16:55.972 R[60761:459244659] 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:121-125 [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