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### Running command:
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###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:struct.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings struct_1.19.0.tar.gz
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/struct.Rcheck'
* using R Under development (unstable) (2025-03-01 r87860 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'struct/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'struct' version '1.19.0'
* 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 'struct' 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 ... OK
* checking Rd files ... NOTE
checkRd: (-1) set_obj_show.Rd:12: Lost braces
    12 | \item{extra_string}{a function that returns an extra string using the input object as an input e.g. function(object){return = 'extra_string'}}
       |                                                                                                                     ^
* 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 ... OK
* 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:
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-ontology.R:50:5'): ontology works as expected ──────────────────
  Error in `grepl(as.character(pattern), x, ignore.case, FALSE, perl, fixed, 
      useBytes, FALSE)`: NA in coercion to boolean
  Backtrace:
      â–†
   1. └─testthat::expect_output(show(O[1]), "STATO:0000555", regexp = "STATO:0000555") at test-ontology.R:50:5
   2.   └─testthat::expect_match(...)
   3.     └─testthat:::expect_match_(...)
   4.       └─base::grepl(regexp, act$val, perl = perl, fixed = fixed, ...)
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 145 ]
  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: 1 ERROR, 1 NOTE
See
  'E:/biocbuild/bbs-3.21-bioc/meat/struct.Rcheck/00check.log'
for details.