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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_1.3.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/bedbaser.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* 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 ‘1.3.0’
* 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 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
.get_url: no visible binding for global variable ‘access_methods’
.get_url: no visible binding for global variable ‘access_url’
.get_url: no visible binding for global variable ‘name’
.get_url: no visible binding for global variable ‘access_id’
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:
  access_id access_methods access_url 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_bed_text_search
> ### Title: Search BED files by text
> ### Aliases: bb_bed_text_search
> 
> ### ** Examples
> 
> bedbase <- BEDbase()
129768 BED files available.
> bb_bed_text_search(bedbase, "hg38")
Error in recs$count : $ operator is invalid for atomic vectors
Calls: bb_bed_text_search
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:
  downloaded 467 KB
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 49 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-bedbaser.R:85:5'): bb_bed_text_search returns results scored against the query ──
  Error in `recs$count`: $ operator is invalid for atomic vectors
  Backtrace:
      ▆
   1. └─bedbaser::bb_bed_text_search(bedbase, "hg38") at test-bedbaser.R:85:5
  
  [ 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 ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘bedbaser.Rmd’ using rmarkdown

Quitting from bedbaser.Rmd:107-109 [bb_search]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `recs$count`:
! $ operator is invalid for atomic vectors
---
Backtrace:
    ▆
 1. └─bedbaser::bb_bed_text_search(bedbase, "cancer", limit = 10)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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 ‘1.3.0’
** 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 Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
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-85.R
trying URL 'https://api.bedbase.org/v1/files/files/8/d/8db1163c16242cd48e839032596ca5be.bed.gz'
Content type 'binary/octet-stream' length 61899 bytes (60 KB)
==================================================
downloaded 60 KB

trying URL 'https://api.bedbase.org/v1/files/files/6/8/683e47db3b317c8ba512807f1ad8baf3.bed.gz'
Content type 'binary/octet-stream' length 741456 bytes (724 KB)
==================================================
downloaded 724 KB

trying URL 'https://api.bedbase.org/v1/files/files/a/4/a480c7e93d49cb5d7a9352bd8fe7b5ee.bed.gz'
Content type 'binary/octet-stream' length 558555 bytes (545 KB)
==================================================
downloaded 545 KB

trying URL 'https://api.bedbase.org/v1/files/files/b/4/b41699ba1e8c91128c9839e3ebecb6aa.bed.gz'
Content type 'binary/octet-stream' length 963741 bytes (941 KB)
==================================================
downloaded 941 KB

trying URL 'https://api.bedbase.org/v1/files/files/b/b/bbad85f21962bb8d972444f7f9a3a932.bed.gz'
Content type 'binary/octet-stream' length 641053 bytes (626 KB)
==================================================
downloaded 626 KB

trying URL 'https://api.bedbase.org/v1/files/files/f/4/f42a7b953b95e8bfa75fb518f8652e97.bed.gz'
Content type 'binary/octet-stream' length 3654780 bytes (3.5 MB)
==================================================
downloaded 3.5 MB

trying URL 'https://api.bedbase.org/v1/files/files/0/6/0692dfe199d26353af23dcbf354a6548.bed.gz'
Content type 'binary/octet-stream' length 478938 bytes (467 KB)
==================================================
downloaded 467 KB

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 49 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-bedbaser.R:85:5'): bb_bed_text_search returns results scored against the query ──
Error in `recs$count`: $ operator is invalid for atomic vectors
Backtrace:
    ▆
 1. └─bedbaser::bb_bed_text_search(bedbase, "hg38") at test-bedbaser.R:85:5

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