##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:rols.install-out.txt --library=E:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings rols_3.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.19-bioc/meat/rols.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'rols/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rols' version '3.0.0'
* 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 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: CVParam
> ### Title: Controlled Vocabulary
> ### Aliases: CVParam charIsCVParam cvCharToCVPar as.character.CVParam
> ###   show,CVParam-method rep,CVParam-method
> 
> ### ** Examples
> 
> 
> ## User param
> CVParam(name = "A user param", value = "the value")
[, , A user param, the value] 
> ## CVParam ESI from PSI's Mass Spectrometry ontology
> Term("MS", "MS:1000073")
Error in (function (cond)  : 
  error in evaluating the argument 'object' in selecting a method for function 'Term': HTTP 500 Internal Server Error.
Calls: Term ... abort -> signal_abort -> signalCondition -> <Anonymous>
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:
   21. │                 │ └─httr2:::check_response(resp)
   22. │                 │   └─httr2:::is_response(resp)
   23. │                 └─httr2::req_perform(request(url))
   24. │                   └─httr2:::handle_resp(req, resp, error_call = error_call)
   25. │                     └─httr2:::resp_abort(resp, req, body, call = error_call)
   26. │                       └─rlang::abort(...)
   27. │                         └─rlang:::signal_abort(cnd, .file)
   28. │                           └─base::signalCondition(cnd)
   29. ├─base (local) `<fn>`(`<ht2__500>`)
   30. └─base::.handleSimpleError(...)
   31.   └─base (local) h(simpleError(msg, call))
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 115 ]
  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
  'E:/biocbuild/bbs-3.19-bioc/meat/rols.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL rols
###
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* installing to library 'E:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'rols' ...
** 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 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 3.0.0 

> 
> test_check("rols")
[, , Hello, World] 
Object of class 'OlsSearch':
  ontolgy: GO 
  query: cell 
  requested: 20 (out of 10498)
  response(s): 0 
Object of class 'Ontologies' with 257 entries
   ADO, AfPO ... CCF, CPONT 
Object of class 'Ontologies' with 1 entries
ADO 
Object of class 'Ontologies' with 2 entries
ADO, AfPO 
Object of class 'Ontologies' with 3 entries
ADO, AfPO, AGRO 
Object of class 'Ontologies' with 4 entries
ADO, AfPO, AGRO, AISM 
Object of class 'Ontologies' with 5 entries
   ADO, AfPO ... AISM, AMPHX 
Ontology: 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: 2024-07-11 Updated: 2024-07-11 Version: 2024-06-17 
   83855 terms  367 properties  18 individuals
Object of class 'Properties' with 91 entries
 From the SO ontology
  definition, IAO_0000231 ... label, deprecated 
Object of class 'Properties' with 160 entries
 From the UBERON ontology
  hepatobiliary system, exocrine system ... liver serosa, liver subserosa 
A Property from the UBERON ontology: UBERON:0002423 
 Label: hepatobiliary system
Object of class 'Terms' with 2736 entries
 From the SO ontology
  SO:0001959, SO:0001960 ... SO:0001957, SO:0001958 
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 3 | WARN 0 | SKIP 0 | PASS 115 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_CVParam.R:6:15'): User param creation ──────────────────────────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'termLabel': error in evaluating the argument 'object' in selecting a method for function 'Term': HTTP 500 Internal Server Error.
Backtrace:
     ▆
  1. ├─testthat::expect_warning(as("[MS, MS:1000073, ESI, ]", "CVParam")) at test_CVParam.R:6:15
  2. │ └─testthat:::quasi_capture(...)
  3. │   ├─testthat (local) .capture(...)
  4. │   │ └─base::withCallingHandlers(...)
  5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  6. ├─methods::as("[MS, MS:1000073, ESI, ]", "CVParam")
  7. │ └─rols (local) asMethod(object)
  8. │   ├─base::lapply(from, cvCharToCVPar)
  9. │   └─base::lapply(from, cvCharToCVPar)
 10. │     └─rols (local) FUN(X[[i]], ...)
 11. │       └─rols::CVParam(label = from[1], accession = from[2])
 12. │         ├─rols::termLabel(Term(label, accession))
 13. │         ├─rols::Term(label, accession)
 14. │         └─rols::Term(label, accession)
 15. │           └─rols (local) .local(object, ...)
 16. │             ├─rols::Term(Ontology(object), id)
 17. │             ├─BiocGenerics::Ontology(object)
 18. │             └─rols::Ontology(object)
 19. │               └─rols:::makeOntology(url)
 20. │                 ├─rols:::ontologyFromJson(resp_body_json(req_perform(request(url))))
 21. │                 │ └─rols:::.Ontology(...)
 22. │                 │   └─methods::new(`<chr>`, ...)
 23. │                 │     ├─methods::initialize(value, ...)
 24. │                 │     └─methods::initialize(value, ...)
 25. │                 ├─httr2::resp_body_json(req_perform(request(url)))
 26. │                 │ └─httr2:::check_response(resp)
 27. │                 │   └─httr2:::is_response(resp)
 28. │                 └─httr2::req_perform(request(url))
 29. │                   └─httr2:::handle_resp(req, resp, error_call = error_call)
 30. │                     └─httr2:::resp_abort(resp, req, body, call = error_call)
 31. │                       └─rlang::abort(...)
 32. │                         └─rlang:::signal_abort(cnd, .file)
 33. │                           └─base::signalCondition(cnd)
 34. ├─base (local) `<fn>`(`<ht2__500>`)
 35. └─base::.handleSimpleError(...)
 36.   └─base (local) h(simpleError(msg, call))
── Error ('test_CVParam.R:20:15'): CVParam creation and coercion ───────────────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'termLabel': error in evaluating the argument 'object' in selecting a method for function 'Term': HTTP 500 Internal Server Error.
Backtrace:
     ▆
  1. ├─rols::CVParam(label = "MS", accession = "MS:1000073") at test_CVParam.R:20:15
  2. │ ├─rols::termLabel(Term(label, accession))
  3. │ ├─rols::Term(label, accession)
  4. │ └─rols::Term(label, accession)
  5. │   └─rols (local) .local(object, ...)
  6. │     ├─rols::Term(Ontology(object), id)
  7. │     ├─BiocGenerics::Ontology(object)
  8. │     └─rols::Ontology(object)
  9. │       └─rols:::makeOntology(url)
 10. │         ├─rols:::ontologyFromJson(resp_body_json(req_perform(request(url))))
 11. │         │ └─rols:::.Ontology(...)
 12. │         │   └─methods::new(`<chr>`, ...)
 13. │         │     ├─methods::initialize(value, ...)
 14. │         │     └─methods::initialize(value, ...)
 15. │         ├─httr2::resp_body_json(req_perform(request(url)))
 16. │         │ └─httr2:::check_response(resp)
 17. │         │   └─httr2:::is_response(resp)
 18. │         └─httr2::req_perform(request(url))
 19. │           └─httr2:::handle_resp(req, resp, error_call = error_call)
 20. │             └─httr2:::resp_abort(resp, req, body, call = error_call)
 21. │               └─rlang::abort(...)
 22. │                 └─rlang:::signal_abort(cnd, .file)
 23. │                   └─base::signalCondition(cnd)
 24. ├─base (local) `<fn>`(`<ht2__500>`)
 25. └─base::.handleSimpleError(...)
 26.   └─base (local) h(simpleError(msg, call))
── Error ('test_CVParam.R:39:15'): Convert char to CVParam ─────────────────────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'termLabel': error in evaluating the argument 'object' in selecting a method for function 'Term': HTTP 500 Internal Server Error.
Backtrace:
     ▆
  1. ├─methods::as(x, "CVParam") at test_CVParam.R:39:15
  2. │ └─rols (local) asMethod(object)
  3. │   ├─base::lapply(from, cvCharToCVPar)
  4. │   └─base::lapply(from, cvCharToCVPar)
  5. │     └─rols (local) FUN(X[[i]], ...)
  6. │       └─rols::CVParam(label = from[1], accession = from[2])
  7. │         ├─rols::termLabel(Term(label, accession))
  8. │         ├─rols::Term(label, accession)
  9. │         └─rols::Term(label, accession)
 10. │           └─rols (local) .local(object, ...)
 11. │             ├─rols::Term(Ontology(object), id)
 12. │             ├─BiocGenerics::Ontology(object)
 13. │             └─rols::Ontology(object)
 14. │               └─rols:::makeOntology(url)
 15. │                 ├─rols:::ontologyFromJson(resp_body_json(req_perform(request(url))))
 16. │                 │ └─rols:::.Ontology(...)
 17. │                 │   └─methods::new(`<chr>`, ...)
 18. │                 │     ├─methods::initialize(value, ...)
 19. │                 │     └─methods::initialize(value, ...)
 20. │                 ├─httr2::resp_body_json(req_perform(request(url)))
 21. │                 │ └─httr2:::check_response(resp)
 22. │                 │   └─httr2:::is_response(resp)
 23. │                 └─httr2::req_perform(request(url))
 24. │                   └─httr2:::handle_resp(req, resp, error_call = error_call)
 25. │                     └─httr2:::resp_abort(resp, req, body, call = error_call)
 26. │                       └─rlang::abort(...)
 27. │                         └─rlang:::signal_abort(cnd, .file)
 28. │                           └─base::signalCondition(cnd)
 29. ├─base (local) `<fn>`(`<ht2__500>`)
 30. └─base::.handleSimpleError(...)
 31.   └─base (local) h(simpleError(msg, call))

[ FAIL 3 | WARN 0 | SKIP 0 | PASS 115 ]
Error: Test failures
Execution halted