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### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:bugsigdbr.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings bugsigdbr_1.17.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/bugsigdbr.Rcheck’
* using R Under development (unstable) (2026-03-05 r89546)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-03-11 01:33:34 UTC
* checking for file ‘bugsigdbr/DESCRIPTION’ ... OK
* this is package ‘bugsigdbr’ version ‘1.17.2’
* 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 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 loading without being on the library search path ... 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
subsetByOntology 7.727  0.046   8.058
restrictTaxLevel 7.367  0.293   7.887
* 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:
  ── Failure ('test-getMetaSignatures.R:72:5'): ... ──────────────────────────────
  Expected `all(grepl("^[A-Za-z ]+$", names(s)))` to be TRUE.
  Differences:
  `actual`:   FALSE
  `expected`: TRUE 
  
  Backtrace:
      ▆
   1. └─bugsigdbr (local) checkSigs(sigs, tax.id.type = "taxname") at test-getMetaSignatures.R:72:5
   2.   └─testthat::expect_true(all(grepl("^[A-Za-z ]+$", names(s)))) at test-getMetaSignatures.R:16:5
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 225 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/bugsigdbr.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL bugsigdbr
###
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘bugsigdbr’ ...
** this is package ‘bugsigdbr’ version ‘1.17.2’
** using staged installation
** R
** inst
** 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 Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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")
Saving _problems/test-getMetaSignatures-72.R



[ FAIL 1 | WARN 0 | SKIP 0 | PASS 225 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-getMetaSignatures.R:72:5'): ... ──────────────────────────────
Expected `all(grepl("^[A-Za-z ]+$", names(s)))` to be TRUE.
Differences:
`actual`:   FALSE
`expected`: TRUE 

Backtrace:
    ▆
 1. └─bugsigdbr (local) checkSigs(sigs, tax.id.type = "taxname") at test-getMetaSignatures.R:72:5
 2.   └─testthat::expect_true(all(grepl("^[A-Za-z ]+$", names(s)))) at test-getMetaSignatures.R:16:5

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 225 ]
Error:
! Test failures.
Execution halted