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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:bedbaser.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings bedbaser_1.3.6.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/bedbaser.Rcheck’
* using R version 4.6.0 alpha (2026-04-05 r89794)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-04-09 01:38:35 UTC
* checking for file ‘bedbaser/DESCRIPTION’ ... OK
* this is package ‘bedbaser’ version ‘1.3.6’
* 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 ... ERROR
Running examples in ‘bedbaser-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bb_list_beds
> ### Title: List BEDs
> ### Aliases: bb_list_beds
> 
> ### ** Examples
> 
> bedbase <- BEDbase()
195669 BED files available.
> bb_list_beds(bedbase)
Error in recs$count : $ operator is invalid for atomic vectors
Calls: bb_list_beds
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:
  Error in `ex_bed$id`: $ operator is invalid for atomic vectors
  Backtrace:
      ▆
   1. └─bedbaser:::.get_file(bedbase, ex_bed$id, tempdir()) at test-utils.R:13:5
   2.   ├─httr::content(bedbase$get_bed_files_v1_bed__bed_id__metadata_files_get(id))
   3.   │ ├─base::stopifnot(is.response(x))
   4.   │ └─httr:::is.response(x)
   5.   └─bedbase$get_bed_files_v1_bed__bed_id__metadata_files_get(id)
   6.     └─rapiclient:::.api_args(formals(), environment())
   7.       └─base::mget(arg_names, environment)
  
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 41 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘bedbaser.Rmd’ using rmarkdown

Quitting from bedbaser.Rmd:85-89 [bb_list_beds]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `recs$count`:
! $ operator is invalid for atomic vectors
---
Backtrace:
    ▆
 1. └─bedbaser::bb_list_beds(bedbase)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'bedbaser.Rmd' failed with diagnostics:
$ operator is invalid for atomic vectors
--- failed re-building ‘bedbaser.Rmd’

SUMMARY: processing the following file failed:
  ‘bedbaser.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 3 ERRORs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/bedbaser.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL bedbaser
###
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘bedbaser’ ...
** this is package ‘bedbaser’ version ‘1.3.6’
** 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 4.6.0 alpha (2026-04-05 r89794)
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.

> # 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-141.R
Saving _problems/test-bedbaser-156.R
Saving _problems/test-cache-41.R
Saving _problems/test-utils-13.R
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 41 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-bedbaser.R:141:5'): bb_to_granges returns GRanges object given bed4+2 with genome ──
Error in `recs$count`: $ operator is invalid for atomic vectors
Backtrace:
    ▆
 1. └─bedbaser::bb_list_beds(bedbase, bed_compliance = "bed4+2") at test-bedbaser.R:141:5
── Error ('test-bedbaser.R:156:5'): bb_to_granges allows passing extra_cols ────
Error in `recs$count`: $ operator is invalid for atomic vectors
Backtrace:
    ▆
 1. └─bedbaser::bb_list_beds(bedbase, bed_compliance = "bed6+5") at test-bedbaser.R:156:5
── Error ('test-cache.R:41:5'): bed files are cached ───────────────────────────
Error in `bb_example(bedbase, "bed")$id`: $ operator is invalid for atomic vectors
── Error ('test-utils.R:13:5'): .get_file returns a valid file path ────────────
Error in `ex_bed$id`: $ operator is invalid for atomic vectors
Backtrace:
    ▆
 1. └─bedbaser:::.get_file(bedbase, ex_bed$id, tempdir()) at test-utils.R:13:5
 2.   ├─httr::content(bedbase$get_bed_files_v1_bed__bed_id__metadata_files_get(id))
 3.   │ ├─base::stopifnot(is.response(x))
 4.   │ └─httr:::is.response(x)
 5.   └─bedbase$get_bed_files_v1_bed__bed_id__metadata_files_get(id)
 6.     └─rapiclient:::.api_args(formals(), environment())
 7.       └─base::mget(arg_names, environment)

[ FAIL 4 | WARN 0 | SKIP 0 | PASS 41 ]
Error:
! Test failures.
Execution halted