##############################################################################
##############################################################################
###
### 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_2.30.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/rols.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rols/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rols’ version ‘2.30.2’
* 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 R 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 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:
    5.     │ └─rols:::.Ontology(...)
    6.     │   └─methods::new(`<chr>`, ...)
    7.     │     ├─methods::initialize(value, ...)
    8.     │     └─methods::initialize(value, ...)
    9.     ├─httr2::resp_body_json(req_perform(request(url)))
   10.     │ └─httr2:::check_response(resp)
   11.     │   └─httr2:::is_response(resp)
   12.     └─httr2::req_perform(request(url))
   13.       └─httr2:::handle_resp(req, resp, error_call = error_call)
   14.         └─httr2:::resp_abort(resp, req, body, call = error_call)
   15.           └─rlang::abort(...)
  
  [ FAIL 12 | WARN 0 | SKIP 0 | PASS 12 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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-3.18-bioc/meat/rols.Rcheck/00check.log’
for details.