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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:bedbaser.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings bedbaser_1.2.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/bedbaser.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘bedbaser/DESCRIPTION’ ... OK
* this is package ‘bedbaser’ version ‘1.2.1’
* 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_grangeslist 14.606  1.164  40.734
bb_to_granges     14.141  0.800  20.854
BEDbase            1.098  0.012   5.824
bb_list_bedsets    0.460  0.120   6.663
* 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:
    "metadata.annotation.target"
    "metadata.annotation.treatment"
    "metadata.annotation.global_sample_id"
  - "metadata.annotation.global_experiment_id"
  - "metadata.annotation.original_file_name"
  - "metadata.processed"
    "metadata.annotation.global_experiment_id1"
    "metadata.annotation.global_experiment_id2"
  + "metadata.annotation.original_file_name"
  + "metadata.processed"
  and 3 more ...
  
  [ 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* 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/R/R/bin/R CMD INSTALL bedbaser
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘bedbaser’ ...
** this is package ‘bedbaser’ version ‘1.2.1’
** 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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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")
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 50 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-bedbaser.R:97:5'): bb_bed_text_search returns results scored against the query ──
`ex_beds` (`actual`) not equal to `beds` (`expected`).

     names(actual)             | names(expected)                         
 [9] "payload.treatment"       | "payload.treatment"       [9]           
[10] "payload.assay"           | "payload.assay"           [10]          
[11] "payload.genome_alias"    | "payload.genome_alias"    [11]          
[12] "payload.genome_digest"   -                                         
[13] "payload.species_name"    | "payload.species_name"    [12]          
[14] "score"                   | "score"                   [13]          
[15] "metadata.name"           | "metadata.name"           [14]          
[16] "metadata.genome_alias"   | "metadata.genome_alias"   [15]          
[17] "metadata.genome_digest"  -                                         
[18] "metadata.bed_compliance" | "metadata.bed_compliance" [16]          
 ... ...                         ...                       and 2 more ...

names(actual)[39:46] vs names(expected)[37:46]
  "metadata.annotation.target"
  "metadata.annotation.treatment"
  "metadata.annotation.global_sample_id"
- "metadata.annotation.global_experiment_id"
- "metadata.annotation.original_file_name"
- "metadata.processed"
  "metadata.annotation.global_experiment_id1"
  "metadata.annotation.global_experiment_id2"
+ "metadata.annotation.original_file_name"
+ "metadata.processed"
and 3 more ...

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