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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:bedbaser.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings bedbaser_1.2.5.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/bedbaser.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘bedbaser/DESCRIPTION’ ... OK
* this is package ‘bedbaser’ version ‘1.2.5’
* 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 ‘bedbaser’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
bb_list_bedsets: no visible binding for global variable ‘bed_ids’
bb_list_bedsets: no visible binding for global variable ‘id’
bb_list_bedsets: no visible binding for global variable ‘name’
bb_list_bedsets: no visible binding for global variable ‘md5sum’
bb_list_bedsets: no visible binding for global variable
  ‘submission_date’
bb_list_bedsets: no visible binding for global variable
  ‘last_update_date’
bb_list_bedsets: no visible binding for global variable ‘description’
bb_list_bedsets: no visible binding for global variable ‘author’
Undefined global functions or variables:
  author bed_ids description id last_update_date md5sum name
  submission_date
* 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
bb_to_grangeslist  15.525  2.286  32.964
bb_to_granges      11.783  0.579  14.568
bb_list_bedsets     0.274  0.041   5.711
bb_bed_text_search  0.211  0.027   6.182
* 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:
  
  `actual$bedsets[[2]]$name`:   "gse135808"
  `expected$bedsets[[2]]$name`: "gse190284"
  
  lines(actual$bedsets[[2]]$description) vs lines(expected$bedsets[[2]]$description)
  - "Data from [GEO GSE135808](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135808)"
  + "Data from [GEO GSE190284](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE190284)"
  - "Topoisomerase 1 Nicking-dependent HP1gamma Engagement Mediates Acute Activation of Phase-separated Enhancers"
  + "Reading the Covalent Topoisomerase1-DNA Intermediate: A Transcriptional Code Broadly Required for Signal-dependent Enhancer Activation [Human CUT&RUN]"
  
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 49 ]
  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, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/bedbaser.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL bedbaser
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘bedbaser’ ...
** this is package ‘bedbaser’ version ‘1.2.5’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘tags’ from package ‘AnVIL’ in package ‘bedbaser’
** 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 (bedbaser)

R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(bedbaser)
> 
> test_check("bedbaser")
Saving _problems/test-bedbaser-23.R
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 49 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-bedbaser.R:23:5'): bb_metadata returns metadata for BEDs ─────
Expected `ex_metadata` to equal `bed_metadata`.
Differences:
`actual$bedsets[[1]]$id`:   "gse190284"
`expected$bedsets[[1]]$id`: "gse135808"

`actual$bedsets[[1]]$name`:   "gse190284"
`expected$bedsets[[1]]$name`: "gse135808"

lines(actual$bedsets[[1]]$description) vs lines(expected$bedsets[[1]]$description)
- "Data from [GEO GSE190284](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE190284)"
+ "Data from [GEO GSE135808](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135808)"
- "Reading the Covalent Topoisomerase1-DNA Intermediate: A Transcriptional Code Broadly Required for Signal-dependent Enhancer Activation [Human CUT&RUN]"
+ "Topoisomerase 1 Nicking-dependent HP1gamma Engagement Mediates Acute Activation of Phase-separated Enhancers"

`actual$bedsets[[2]]$id`:   "gse135808"
`expected$bedsets[[2]]$id`: "gse190284"

`actual$bedsets[[2]]$name`:   "gse135808"
`expected$bedsets[[2]]$name`: "gse190284"

lines(actual$bedsets[[2]]$description) vs lines(expected$bedsets[[2]]$description)
- "Data from [GEO GSE135808](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135808)"
+ "Data from [GEO GSE190284](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE190284)"
- "Topoisomerase 1 Nicking-dependent HP1gamma Engagement Mediates Acute Activation of Phase-separated Enhancers"
+ "Reading the Covalent Topoisomerase1-DNA Intermediate: A Transcriptional Code Broadly Required for Signal-dependent Enhancer Activation [Human CUT&RUN]"


[ FAIL 1 | WARN 0 | SKIP 0 | PASS 49 ]
Error:
! Test failures.
Execution halted