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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_3.5.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/rols.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* 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 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rols/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rols’ version ‘3.5.0’
* 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 ‘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: Ontologies
> ### Title: Ontologies
> ### Aliases: Ontologies Ontology olsLinks olsLinks,Ontology olsConfig
> ###   olsConfig,Ontology olsVersion olsVersion,character
> ###   olsVersion,Ontology olsVersion,Ontologies olsLoaded
> ###   olsLoaded,character olsLoaded,Ontology olsLoaded,Ontologies
> ###   olsUpdated olsUpdated,character olsUpdated,Ontology
> ###   olsUpdated,Ontologies olsStatus olsStatus,character
> ###   olsStatus,Ontology olsStatus,Ontologies olsPrefix olsPrefix,character
> ###   olsPrefix,Ontology olsPrefix,Ontologies olsDesc olsDesc,character
> ###   olsDesc,Ontology olsDesc,Ontologies olsTitle olsTitle,character
> ###   olsTitle,Ontology olsTitle,Ontologies olsNamespace
> ###   olsNamespace,character olsNamespace,Ontology olsNamespace,Ontologies
> ###   ontologyUrl ontologyUrl,character ontologyUrl,Ontology
> ###   as.data.frame.Ontologies Ontologies,missing-method
> ###   Ontology,character-method Ontology,Ontology-method
> ###   show,Ontology-method show,Ontologies-method
> ###   olsVersion,character-method olsVersion,Ontology-method
> ###   olsVersion,Ontologies-method olsLoaded,character-method
> ###   olsLoaded,Ontology-method olsLoaded,Ontologies-method
> ###   olsLinks,Ontology-method olsConfig,Ontology-method
> ###   olsUpdated,character-method olsUpdated,Ontology-method
> ###   olsUpdated,Ontologies-method olsPrefix,character-method
> ###   olsPrefix,Ontology-method olsPrefix,Ontologies-method
> ###   olsDesc,character-method olsDesc,Ontology-method
> ###   olsDesc,Ontologies-method olsTitle,character-method
> ###   olsTitle,Ontology-method olsTitle,Ontologies-method
> ###   olsStatus,character-method olsStatus,Ontology-method
> ###   olsStatus,Ontologies-method olsNamespace,character-method
> ###   olsNamespace,Ontology-method olsNamespace,Ontologies-method
> ###   ontologyUrl,character-method ontologyUrl,Ontology-method
> ###   lapply,Ontologies-method [,Ontologies-method [[,Ontologies-method
> ###   length,Ontologies-method
> 
> ### ** Examples
> 
> 
> #############################
> ## All ontologies
> (onts <- Ontologies())
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'X' in selecting a method for function 'lapply': error in evaluating the argument 'X' in selecting a method for function 'lapply': HTTP 404 Not Found.
Calls: Ontologies ... signalCondition -> <Anonymous> -> .handleSimpleError -> h
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:
   16. │       │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
   17. │       ├─rlang::try_fetch(...)
   18. │       │ └─base::withCallingHandlers(...)
   19. │       └─httr2::req_perform(req, path = get_path(i), mock = mock)
   20. │         └─httr2:::handle_resp(req, resp, error_call = error_call)
   21. │           └─rlang::cnd_signal(cnd)
   22. │             └─rlang:::signal_abort(cnd)
   23. │               └─base::signalCondition(cnd)
   24. ├─base (local) `<fn>`(`<ht2__404>`)
   25. └─base::.handleSimpleError(...)
   26.   └─base (local) h(simpleError(msg, call))
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 77 ]
  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
See
  ‘/Users/biocbuild/bbs-3.22-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/4.5-arm64/Resources/library’
* installing *source* package ‘rols’ ...
** this is package ‘rols’ version ‘3.5.0’
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (rols)

R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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 3.5.0 

> 
> test_check("rols")
[, , Hello, World] 
Object of class 'OlsSearch':
  ontolgy: GO 
  query: cell 
  requested: 20 (out of 10602)
  response(s): 0 
Object of class 'Properties' with 92 entries
 From the SO ontology
  definition, IAO_0000231 ... label, deprecated 
Object of class 'Properties' with 164 entries
 From the UBERON ontology
  hepatobiliary system, exocrine system ... quadrate lobe of liver, hepatic portal fibroblast 
A Property from the UBERON ontology: UBERON:0002423 
 Label: hepatobiliary system
Object of class 'Terms' with 2745 entries
 From the SO ontology
  SO:0000398, SO:0000399 ... SO:0000396, SO:0000397 
A Term 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 1 | WARN 0 | SKIP 0 | PASS 77 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_Onologies.R:1:1'): (code run outside of `test_that()`) ─────────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'X' in selecting a method for function 'lapply': error in evaluating the argument 'X' in selecting a method for function 'lapply': HTTP 404 Not Found.
Backtrace:
     ▆
  1. ├─rols::Ontologies() at test_Onologies.R:1:1
  2. ├─rols::Ontologies()
  3. │ └─rols:::makeOntologies()
  4. │   ├─rols:::.Ontologies(...)
  5. │   │ └─methods::new(`<chr>`, ...)
  6. │   │   ├─methods::initialize(value, ...)
  7. │   │   └─methods::initialize(value, ...)
  8. │   ├─base::lapply(ols_requests(url, "ontologies"), ontologyFromJson)
  9. │   └─rols:::ols_requests(url, "ontologies")
 10. │     ├─base::unlist(...)
 11. │     ├─base::lapply(...)
 12. │     └─httr2::req_perform_iterative(...)
 13. │       ├─base::tryCatch(...)
 14. │       │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 15. │       │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 16. │       │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 17. │       ├─rlang::try_fetch(...)
 18. │       │ └─base::withCallingHandlers(...)
 19. │       └─httr2::req_perform(req, path = get_path(i), mock = mock)
 20. │         └─httr2:::handle_resp(req, resp, error_call = error_call)
 21. │           └─rlang::cnd_signal(cnd)
 22. │             └─rlang:::signal_abort(cnd)
 23. │               └─base::signalCondition(cnd)
 24. ├─base (local) `<fn>`(`<ht2__404>`)
 25. └─base::.handleSimpleError(...)
 26.   └─base (local) h(simpleError(msg, call))

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 77 ]
Error: Test failures
Execution halted