##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:bedbaser.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings bedbaser_1.0.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/bedbaser.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘1.0.3’
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
bb_to_granges     13.815  1.083  16.822
bb_to_grangeslist 13.935  0.835  22.268
bb_list_bedsets    0.355  0.116   5.627
* 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:
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 50 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-bedbaser.R:128:5'): bb_to_granges returns GRanges object given bed4+2 with genome ──
  Error in `.get_extra_cols(file_path, metadata$compliant_columns, metadata$non_compliant_columns)`: x + y == dim(t)[2] is not TRUE
  Backtrace:
      ▆
   1. └─bedbaser::bb_to_granges(bedbase, id) at test-bedbaser.R:128:5
   2.   └─bedbaser:::.bed_file_to_granges(...)
   3.     └─bedbaser:::.get_extra_cols(...)
   4.       └─base::stopifnot(x + y == dim(t)[2])
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 50 ]
  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-3.21-bioc/meat/bedbaser.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL bedbaser
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘bedbaser’ ...
** this is package ‘bedbaser’ version ‘1.0.3’
** 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 4.5.1 (2025-06-13) -- "Great Square Root"
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")
trying URL 'https://api.bedbase.org/v1/files/files/b/7/b74684c977d4acc2f305806776d06089.bed.gz'
Content type 'binary/octet-stream' length 20667 bytes (20 KB)
==================================================
downloaded 20 KB

trying URL 'https://api.bedbase.org/v1/files/files/c/c/ccfc6fe8b7e310be361a2b3425508715.bed.gz'
Content type 'binary/octet-stream' length 1272478 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

trying URL 'https://api.bedbase.org/v1/files/files/d/e/de5ddaf95916b3c70fb7cbe04bf8148f.bed.gz'
Content type 'binary/octet-stream' length 18487976 bytes (17.6 MB)
==================================================
downloaded 17.6 MB

trying URL 'https://api.bedbase.org/v1/files/files/e/e/ee46cd046441d2702fd44a084d87adb9.bed.gz'
Content type 'binary/octet-stream' length 1221513 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

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/8/6/86434866aac1ab8bd16ac9d274f2c468.bed.gz'
Content type 'binary/octet-stream' length 2815381 bytes (2.7 MB)
==================================================
downloaded 2.7 MB

trying URL 'https://api.bedbase.org/v1/files/files/4/5/45de30365e4a77f83b77b4cfd989cf06.bed.gz'
Content type 'binary/octet-stream' length 1445709 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 50 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-bedbaser.R:128:5'): bb_to_granges returns GRanges object given bed4+2 with genome ──
Error in `.get_extra_cols(file_path, metadata$compliant_columns, metadata$non_compliant_columns)`: x + y == dim(t)[2] is not TRUE
Backtrace:
    ▆
 1. └─bedbaser::bb_to_granges(bedbase, id) at test-bedbaser.R:128:5
 2.   └─bedbaser:::.bed_file_to_granges(...)
 3.     └─bedbaser:::.get_extra_cols(...)
 4.       └─base::stopifnot(x + y == dim(t)[2])

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 50 ]
Error: Test failures
Execution halted