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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OmicsMLRepoR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OmicsMLRepoR_1.5.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/OmicsMLRepoR.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OmicsMLRepoR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmicsMLRepoR’ version ‘1.5.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘OmicsMLRepoR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.getAllTargetForms: no visible binding for global variable ‘.’
.getOntos: no visible binding for global variable ‘.’
availableTerms: no visible binding for global variable ‘.’
ontoSummarize: no visible global function definition for ‘Ontology’
ontoSummarize: no visible global function definition for ‘Term’
ontoSummarize : <anonymous>: no visible global function definition for
  ‘Term’
ontoTreePlot: no visible global function definition for ‘Ontology’
ontoTreePlot: no visible global function definition for ‘Term’
ontoTreePlot: no visible binding for global variable ‘iri’
ontoTreePlot: no visible binding for global variable ‘text’
ontoTreePlot: no visible binding for global variable ‘parent’
ontoTreePlot: no visible binding for global variable ‘from’
ontoTreePlot: no visible binding for global variable ‘to’
Undefined global functions or variables:
  . Ontology Term from iri parent text to
Consider adding
  importFrom("graphics", "text")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘OmicsMLRepoR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ontoSummarize
> ### Title: Groups ontology terms by the child term of a provided "parent"
> ###   they fall under
> ### Aliases: ontoSummarize
> 
> ### ** Examples
> 
> ontology <- "ncit"
> parent <- "NCIT:C17049"
> descendants <- c("NCIT:C44265", "NCIT:C77811", "NCIT:C43856",
+                  "NCIT:C43672", "NCIT:C2991", "NCIT:C43860")
> ontoSummarize(parent, descendants, ontology)
Error in Ontology(ontology) : could not find function "Ontology"
Calls: ontoSummarize
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > test_check("OmicsMLRepoR")
  Saving _problems/test-ontoTreePlot-6.R
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 33 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-ontoTreePlot.R:6:5'): ontoTreePlot function works correctly ────
  Error in `Ontology(sample_db)`: could not find function "Ontology"
  Backtrace:
      ▆
   1. └─OmicsMLRepoR::ontoTreePlot(test_term) at test-ontoTreePlot.R:6:5
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 33 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/OmicsMLRepoR.Rcheck/00check.log’
for details.