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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:bugsigdbr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings bugsigdbr_1.2.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/bugsigdbr.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘bugsigdbr/DESCRIPTION’ ... OK
* this is package ‘bugsigdbr’ version ‘1.2.2’
* 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 ‘bugsigdbr’ 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 dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘BiocFileCache:::.sql_set_expires’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getMetaSignatures: no visible binding for global variable ‘Abundance in
  Group 1’
Undefined global functions or variables:
  Abundance in Group 1
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
getOntology      6.618  0.363   7.119
subsetByOntology 3.316  0.398   5.221
* 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 ════════════════════════════════════════════════════════════════
  ── Failure ('test-ontology.R:71'): subsetByOntology ────────────────────────────
  all(pos %in% sdf[, col]) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  Backtrace:
      ▆
   1. └─bugsigdbr (local) checkSubset(sdf, "Condition", cpos[[ct]], cneg[[ct]]) at test-ontology.R:71:8
   2.   └─testthat::expect_true(all(pos %in% sdf[, col])) at test-ontology.R:27:4
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 224 ]
  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: 1 ERROR, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/bugsigdbr.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL bugsigdbr
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘bugsigdbr’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** 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 (bugsigdbr)

R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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.

> library(testthat)
> library(bugsigdbr)
> 
> test_check("bugsigdbr")
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 224 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-ontology.R:71'): subsetByOntology ────────────────────────────
all(pos %in% sdf[, col]) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. └─bugsigdbr (local) checkSubset(sdf, "Condition", cpos[[ct]], cneg[[ct]]) at test-ontology.R:71:8
 2.   └─testthat::expect_true(all(pos %in% sdf[, col])) at test-ontology.R:27:4

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 224 ]
Error: Test failures
Execution halted