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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:rols.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings rols_3.7.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/rols.Rcheck’
* using R version 4.6.0 alpha (2026-04-08 r89818)
* using platform: aarch64-apple-darwin23
* R was compiled by
    Apple clang version 17.0.0 (clang-1700.3.19.1)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-04-13 01:51:46 UTC
* using option ‘--no-vignettes’
* checking for file ‘rols/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rols’ version ‘3.7.2’
* 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 ‘rols’ 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 whether startup messages can be suppressed ... 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 ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘rols-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: olsTerms
> ### Title: Ontology Terms
> ### Aliases: olsTerms olsTerm olsTerms,character olsTerms,olsOntology
> ###   termLinks termLinks,olsTerm children parents ancestors descendants
> ###   termSynonym termSynonym,olsTerm termSynonym,olsTerms isObsolete
> ###   isObsolete,olsTerm isObsolete,olsTerms isRoot isRoot,olsTerm
> ###   isRoot,olsTerms termLabel termLabel,olsTerm termLabel,olsTerms termId
> ###   termId,olsTerm termId,olsTerms termPrefix termPrefix,olsTerm
> ###   termPrefix,olsTerms termDesc termDesc,olsTerm termDesc,olsTerms
> ###   termOntology termOntology,olsTerm termOntology,olsTerms termNamespace
> ###   termNamespace,olsTerm termNamespace,olsTerms
> ###   olsTerms,character-method olsTerms,olsOntology-method
> ###   olsTerm,character-method olsTerm,olsOntology-method
> ###   show,olsTerm-method show,olsTerms-method termSynonym,olsTerm-method
> ###   termSynonym,olsTerms-method isObsolete,olsTerm-method
> ###   isObsolete,olsTerms-method isRoot,olsTerm-method
> ###   isRoot,olsTerms-method termLabel,olsTerm-method
> ###   termLabel,olsTerms-method termId,olsTerm-method
> ###   termId,olsTerms-method termLinks,olsTerm-method
> ###   termPrefix,olsTerm-method termPrefix,olsTerms-method
> ###   termDesc,olsTerm-method termDesc,olsTerms-method
> ###   termOntology,olsTerm-method termOntology,olsTerms-method
> ###   termNamespace,olsTerm-method termNamespace,olsTerms-method
> ###   length,olsTerms-method unique,olsTerms-method [,olsTerms-method
> ###   [[,olsTerms-method lapply,olsTerms-method as.olsTerm.data.frame
> ###   as.olsTerms.data.frame
> 
> ### ** Examples
> 
> 
> ## Alzheimer's Disease Ontology (ADO)
> (adoterms <- olsTerms('ado'))
⠙ iterating 1 done (0.24/s) | 4.1s
⠹ iterating 2 done (0.28/s) | 7.1s
Object of class 'olsTerms' with 1513 entries
 From the ADO ontology
  ADO:0000001, ADO:0000010 ... OGG:3000007098, OGG:3000007099 
> 
> ## Focus on squamous epithelium
> (trm <- adoterms[["UBERON:0006914"]])
NULL
> 
> ## Accessors
> termLabel(trm)
Error: unable to find an inherited method for function ‘termLabel’ for signature ‘object = "NULL"’
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
olsProperties 0.283  0.020   7.669
olsOntologies 0.190  0.011   7.895
OlsSearch     0.122  0.011   6.983
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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: 1 ERROR
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/rols.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL rols
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
* installing *source* package ‘rols’ ...
** this is package ‘rols’ version ‘3.7.2’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘lapply’ from package ‘base’ in package ‘rols’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in fun(libname, pkgname) :
  Package 'rols' is deprecated and will be removed from Bioconductor
  version 3.24
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'rols' is deprecated and will be removed from Bioconductor
  version 3.24
** testing if installed package keeps a record of temporary installation path
* DONE (rols)

R version 4.6.0 alpha (2026-04-08 r89818)
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # setting R_TESTS to empty string because of 
> # https://github.com/hadley/testthat/issues/144
> # revert this when that issue in R is fixed.
> Sys.setenv("R_TESTS" = "")
> library("testthat")
> library("rols")

This is 'rols' version 3.7.2 

Warning message:
In fun(libname, pkgname) :
  Package 'rols' is deprecated and will be removed from Bioconductor
  version 3.24
> 
> test_check("rols")
[, , Hello, World] 
Object of class 'OlsSearch':
  ontolgy: GO 
  query: cell 
  requested: 20 (out of 10306)
  response(s): 0 
Object of class 'olsOntologies' with 277 entries
   ADDICTO, ADO ... ZFS, ZP 
Object of class 'olsOntologies' with 1 entries
ADDICTO 
Object of class 'olsOntologies' with 2 entries
ADDICTO, ADO 
Object of class 'olsOntologies' with 3 entries
ADDICTO, ADO, AEO 
Object of class 'olsOntologies' with 4 entries
ADDICTO, ADO, AEO, AFO 
Object of class 'olsOntologies' with 5 entries
   ADDICTO, ADO ... AFO, AfPO 
olsOntology: Gene Ontology (go)  
  The Gene Ontology (GO) provides a framework and set of concepts for
  describing the functions of gene products from all organisms.
   Loaded: 2026-04-10 Updated: 2026-04-10 Version: 2026-03-25 
   84523 terms  480 properties  48 individuals
Object of class 'olsProperties' with 92 entries
 From the SO ontology
  definition, IAO_0000231 ... label, deprecated 
Object of class 'olsProperties' with 164 entries
 From the UBERON ontology
  hepatobiliary system, exocrine gland ... quadrate lobe of liver, hepatic portal fibroblast 
A olsProperty from the UBERON ontology: UBERON:0002423 
 Label: hepatobiliary system
Object of class 'olsTerms' with 2747 entries
 From the SO ontology
  BS:00003, BS:0000338 ... SO:2000061, SO:3000000 
A olsTerm from the GO ontology: GO:0032801 
 Label: receptor catabolic process
  The chemical reactions and pathways resulting in the breakdown of a
  receptor molecule, a macromolecule that undergoes combination with a
  hormone, neurotransmitter, drug or intracellular messenger to initiate
  a change in cell function.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 122 ]
> 
> proc.time()
   user  system elapsed 
  4.963   0.366  74.069