##############################################################################
##############################################################################
###
### 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_1.3.7.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/bedbaser.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* 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: 2026-04-27 01:43:03 UTC
* checking for file ‘bedbaser/DESCRIPTION’ ... OK
* this is package ‘bedbaser’ version ‘1.3.7’
* 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 15.143  0.835  33.461
bb_to_granges     11.597  0.573  14.818
bb_list_bedsets    0.345  0.057   6.081
* 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:
   16.                       └─base::scan(...)
  ── Error ('test-bedbaser.R:145:5'): bb_to_granges returns GRanges object given bed4+2 with genome ──
  Error in `scan(file = file, what = what, sep = sep, quote = quote, dec = dec, nmax = nrows, skip = 0, na.strings = na.strings, quiet = TRUE, fill = fill, strip.white = strip.white, blank.lines.skip = blank.lines.skip, multi.line = FALSE, comment.char = comment.char, allowEscapes = allowEscapes, flush = flush, encoding = encoding, skipNul = skipNul)`: line 948 did not have 8 elements
  Backtrace:
      ▆
   1. └─bedbaser::bb_to_granges(bedbase, id) at test-bedbaser.R:145:5
   2.   └─bedbaser:::.bed_file_to_granges(...)
   3.     └─bedbaser:::.get_extra_cols(...)
   4.       └─utils::read.table(file_path, sep = "\t")
   5.         └─base::scan(...)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 48 ]
  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-3.23-bioc/meat/bedbaser.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL bedbaser
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘bedbaser’ ...
** this is package ‘bedbaser’ version ‘1.3.7’
** 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 RC (2026-04-17 r89917) -- "Because it was There"
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-119.R
Saving _problems/test-bedbaser-145.R
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 48 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-bedbaser.R:119:5'): bb_to_granges returns a GRanges object given a 3+0 bed file ──
Error in `scan(file = file, what = what, sep = sep, quote = quote, dec = dec, nmax = nrows, skip = 0, na.strings = na.strings, quiet = TRUE, fill = fill, strip.white = strip.white, blank.lines.skip = blank.lines.skip, multi.line = FALSE, comment.char = comment.char, allowEscapes = allowEscapes, flush = flush, encoding = encoding, skipNul = skipNul)`: line 1595 did not have 5 elements
Backtrace:
     ▆
  1. └─bedbaser::bb_to_granges(bedbase, id) at test-bedbaser.R:119:5
  2.   └─bedbaser:::.bed_file_to_granges(...)
  3.     └─bedbaser:::.import_with_genome(args)
  4.       └─base::tryCatch(...)
  5.         └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  6.           └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  7.             └─value[[3L]](cond)
  8.               ├─base::do.call(rtracklayer::import, within(args, rm("genome")))
  9.               ├─BiocIO (local) `<stndrdGn>`(con = `<chr>`, format = "bed")
 10.               └─BiocIO (local) `<stndrdGn>`(con = `<chr>`, format = "bed")
 11.                 ├─BiocIO::import(FileForFormat(con, format), ...)
 12.                 └─rtracklayer::import(FileForFormat(con, format), ...)
 13.                   └─rtracklayer (local) .local(con, format, text, ...)
 14.                     ├─S4Vectors::DataFrame(...)
 15.                     └─utils::read.table(...)
 16.                       └─base::scan(...)
── Error ('test-bedbaser.R:145:5'): bb_to_granges returns GRanges object given bed4+2 with genome ──
Error in `scan(file = file, what = what, sep = sep, quote = quote, dec = dec, nmax = nrows, skip = 0, na.strings = na.strings, quiet = TRUE, fill = fill, strip.white = strip.white, blank.lines.skip = blank.lines.skip, multi.line = FALSE, comment.char = comment.char, allowEscapes = allowEscapes, flush = flush, encoding = encoding, skipNul = skipNul)`: line 948 did not have 8 elements
Backtrace:
    ▆
 1. └─bedbaser::bb_to_granges(bedbase, id) at test-bedbaser.R:145:5
 2.   └─bedbaser:::.bed_file_to_granges(...)
 3.     └─bedbaser:::.get_extra_cols(...)
 4.       └─utils::read.table(file_path, sep = "\t")
 5.         └─base::scan(...)

[ FAIL 2 | WARN 0 | SKIP 0 | PASS 48 ]
Error:
! Test failures.
Execution halted