##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:bedbaser.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings bedbaser_1.3.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/bedbaser.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘bedbaser/DESCRIPTION’ ... OK
* this is package ‘bedbaser’ version ‘1.3.1’
* 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 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 5.624  0.169   7.082
bb_to_granges     5.385  0.393   6.857
* 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.global_experiment_id2"
  + "metadata.annotation.global_experiment_id"
    "metadata.annotation.original_file_name"
    "metadata.processed"
  - "payload.genome_digest"
  - "metadata.genome_digest"
  - "metadata.annotation.global_experiment_id"
  + "metadata.annotation.global_experiment_id1"
  + "metadata.annotation.global_experiment_id2"
  
  
  [ 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
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/bedbaser.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL bedbaser
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’
* installing *source* package ‘bedbaser’ ...
** this is package ‘bedbaser’ version ‘1.3.1’
** 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 Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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-97.R

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname


Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit


Attaching package: 'BSgenome.Hsapiens.UCSC.hg19'

The following object is masked from 'package:BSgenome.Hsapiens.UCSC.hg38':

    Hsapiens

[ 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 ──
Expected `ex_beds` to equal `beds`.
Differences:
     names(actual)             | names(expected)                         
 [9] "payload.treatment"       | "payload.treatment"       [9]           
[10] "payload.assay"           | "payload.assay"           [10]          
[11] "payload.genome_alias"    | "payload.genome_alias"    [11]          
                               - "payload.genome_digest"   [12]          
[12] "payload.species_name"    | "payload.species_name"    [13]          
[13] "score"                   | "score"                   [14]          
[14] "metadata.name"           | "metadata.name"           [15]          
[15] "metadata.genome_alias"   | "metadata.genome_alias"   [16]          
                               - "metadata.genome_digest"  [17]          
[16] "metadata.bed_compliance" | "metadata.bed_compliance" [18]          
 ... ...                         ...                       and 2 more ...

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


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