Multiple platform build/check report for BioC 3.23 - CHECK results for bedbaser on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2025-12-22 r89219) -- "Unsuffered Consequences"	4815
kjohnson3	macOS 13.7.7 Ventura	arm64	R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"	4593
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

CHECK results for bedbaser on kjohnson3

To the developers/maintainers of the bedbaser package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/bedbaser.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: bedbaser

Version: 1.3.0

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_1.3.0.tar.gz

StartedAt: 2026-01-06 18:37:39 -0500 (Tue, 06 Jan 2026)

EndedAt: 2026-01-06 18:39:14 -0500 (Tue, 06 Jan 2026)

EllapsedTime: 95.2 seconds

RetCode: 1

Status: ERROR

CheckDir: bedbaser.Rcheck

Warnings: NA

Command output

##############################################################################
##############################################################################
###
### 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_1.3.0.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 ‘1.3.0’
* 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 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     6.249  0.445   7.783
bb_to_grangeslist 4.820  0.179   6.151
* 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:
    NA
    "excluderanges"
  - "excluderanges"
  + NA
  - NA
  + "excluderanges"
    "excluderanges"
    NA
    NA
  
  
  [ 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.

Installation output

bedbaser.Rcheck/00install.out

##############################################################################
##############################################################################
###
### 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 ‘1.3.0’
** 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)

Tests output

bedbaser.Rcheck/tests/testthat.Rout.fail


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-95.R
trying URL 'https://api.bedbase.org/v1/files/files/d/9/d9e14de58e4232008019f8716fd1874b.bed.gz'
Content type 'binary/octet-stream' length 42862 bytes (41 KB)
==================================================
downloaded 41 KB


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

trying URL 'https://api.bedbase.org/v1/files/files/6/5/6523af8df56f91153849a17c585b2a6c.bed.gz'
Content type 'binary/octet-stream' length 18225 bytes (17 KB)
==================================================
downloaded 17 KB

trying URL 'https://api.bedbase.org/v1/files/files/0/4/04bf90b0a5c238e827b1f49c425ebfa4.bed.gz'
Content type 'binary/octet-stream' length 189826 bytes (185 KB)
==================================================
downloaded 185 KB


Attaching package: 'BSgenome.Hsapiens.UCSC.hg38'

The following object is masked from 'package:BSgenome.Hsapiens.UCSC.hg19':

    Hsapiens

trying URL 'https://api.bedbase.org/v1/files/files/f/2/f2b39e39f8a88eb2f97542fb176721b4.bed.gz'
Content type 'binary/octet-stream' length 224369 bytes (219 KB)
==================================================
downloaded 219 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/f46efa29d907d2225040196e9814841a.bed.gz'
Content type 'binary/octet-stream' length 6241 bytes
==================================================
downloaded 6241 bytes

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 50 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-bedbaser.R:95:5'): 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"

    actual$id                          | expected$id                           
[1] "6be4f1fb7464a8c2f68952755652d98b" - "2d86ffa3f593c74382caa04cd26130c5" [1]
[2] "2d86ffa3f593c74382caa04cd26130c5" - "6be4f1fb7464a8c2f68952755652d98b" [2]
[3] "3986a74ae4f05012f5c6e0be54877552" | "3986a74ae4f05012f5c6e0be54877552" [3]
[4] "3d80a48ef0b4a4ce69c48cacdc279242" | "3d80a48ef0b4a4ce69c48cacdc279242" [4]
[5] "388b4b726e760acf59974fd8aa83f1b7" - "5691d9009f96145641f0e3b9ff4f0735" [5]
[6] "5691d9009f96145641f0e3b9ff4f0735" - "388b4b726e760acf59974fd8aa83f1b7" [6]
[7] "2b93bec4ddad5fc2f30597257e7a0560" | "2b93bec4ddad5fc2f30597257e7a0560" [7]
[8] "1b7fc14e60f8affde442e6a061c55877" | "1b7fc14e60f8affde442e6a061c55877" [8]
[9] "9f17013256fca6c57227ba30abc0d99c" | "9f17013256fca6c57227ba30abc0d99c" [9]

    actual$payload.id                  | expected$payload.id                   
[1] "6be4f1fb7464a8c2f68952755652d98b" - "2d86ffa3f593c74382caa04cd26130c5" [1]
[2] "2d86ffa3f593c74382caa04cd26130c5" - "6be4f1fb7464a8c2f68952755652d98b" [2]
[3] "3986a74ae4f05012f5c6e0be54877552" | "3986a74ae4f05012f5c6e0be54877552" [3]
[4] "3d80a48ef0b4a4ce69c48cacdc279242" | "3d80a48ef0b4a4ce69c48cacdc279242" [4]
[5] "388b4b726e760acf59974fd8aa83f1b7" - "5691d9009f96145641f0e3b9ff4f0735" [5]
[6] "5691d9009f96145641f0e3b9ff4f0735" - "388b4b726e760acf59974fd8aa83f1b7" [6]
[7] "2b93bec4ddad5fc2f30597257e7a0560" | "2b93bec4ddad5fc2f30597257e7a0560" [7]
[8] "1b7fc14e60f8affde442e6a061c55877" | "1b7fc14e60f8affde442e6a061c55877" [8]
[9] "9f17013256fca6c57227ba30abc0d99c" | "9f17013256fca6c57227ba30abc0d99c" [9]

actual$payload.name[1:9] vs expected$payload.name[1:9]
- "ChIP_HL60_H3K27ac_WT_rep2"
+ "hg38.Reddy.wgEncodeDacMapabilityConsensusExcludable.hg38"
- "hg38.Reddy.wgEncodeDacMapabilityConsensusExcludable.hg38"
+ "ChIP_HL60_H3K27ac_WT_rep2"
  "ChIP_HL60_H3K27ac_WT_rep1"
  "hg38.UCSC.heterochromatin"
- "hg38.Lareau.hg38.full.Excludable"
+ "ChIP_HL60_H3K4me3_WT_rep2"
- "ChIP_HL60_H3K4me3_WT_rep2"
+ "hg38.Lareau.hg38.full.Excludable"
  "hg38.Nordin.CandRblacklist_hg38"
  "ChIP_HL60_H3K4me3_WT_rep1"
  "HT1376_DMSO_H3K27me3"

actual$payload.description[1:9] vs expected$payload.description[1:9]
- ""
+ "Defined by the ENCODE consortium, includes satellite repeats (CATTC, GAATG, GAGTG, ACRO1), RepeatMasker repeats (ALR/Alpha, BSR/Beta), centromeric repeats, chrM, High/Low mappability islands. Has extra chromosomes, use keepStandardChromosomes() filtering"
- "Defined by the ENCODE consortium, includes satellite repeats (CATTC, GAATG, GAGTG, ACRO1), RepeatMasker repeats (ALR/Alpha, BSR/Beta), centromeric repeats, chrM, High/Low mappability islands. Has extra chromosomes, use keepStandardChromosomes() filtering"
+ ""
  ""
  "Gaps from large blocks of heterochromatin"
- "ENCODE excludable regions combined with regions of high homology to mtDNA (NUMT regions)"
+ ""
- ""
+ "ENCODE excludable regions combined with regions of high homology to mtDNA (NUMT regions)"
  "Defined from CUT&RUN negative controls as 0.1% top significant SEACR peaks in over 30% of samples"
  ""
  ""

    actual$payload.cell_line | expected$payload.cell_line    
[1] "HL-60"                  - ""                         [1]
[2] ""                       - "HL-60"                    [2]
[3] "HL-60"                  | "HL-60"                    [3]
[4] ""                       | ""                         [4]
[5] ""                       - "HL-60"                    [5]
[6] "HL-60"                  - ""                         [6]
[7] ""                       | ""                         [7]
[8] "HL-60"                  | "HL-60"                    [8]
[9] "HT1376"                 | "HT1376"                   [9]

    actual$payload.assay | expected$payload.assay    
[1] "ChIP-Seq"           - ""                     [1]
[2] ""                   - "ChIP-Seq"             [2]
[3] "ChIP-Seq"           | "ChIP-Seq"             [3]
[4] ""                   | ""                     [4]
[5] ""                   - "ChIP-Seq"             [5]
[6] "ChIP-Seq"           - ""                     [6]
[7] ""                   | ""                     [7]
[8] "ChIP-Seq"           | "ChIP-Seq"             [8]
[9] "ChIP-Seq"           | "ChIP-Seq"             [9]

    actual$payload.genome_alias | expected$payload.genome_alias    
[1] "hg19"                      - "hg38"                        [1]
[2] "hg38"                      - "hg19"                        [2]
[3] "hg19"                      | "hg19"                        [3]
[4] "hg38"                      | "hg38"                        [4]
[5] "hg38"                      - "hg19"                        [5]
[6] "hg19"                      - "hg38"                        [6]
[7] "hg38"                      | "hg38"                        [7]
[8] "hg19"                      | "hg19"                        [8]
[9] "hg38"                      | "hg38"                        [9]

actual$metadata.name[1:9] vs expected$metadata.name[1:9]
- "ChIP_HL60_H3K27ac_WT_rep2"
+ "hg38.Reddy.wgEncodeDacMapabilityConsensusExcludable.hg38"
- "hg38.Reddy.wgEncodeDacMapabilityConsensusExcludable.hg38"
+ "ChIP_HL60_H3K27ac_WT_rep2"
  "ChIP_HL60_H3K27ac_WT_rep1"
  "hg38.UCSC.heterochromatin"
- "hg38.Lareau.hg38.full.Excludable"
+ "ChIP_HL60_H3K4me3_WT_rep2"
- "ChIP_HL60_H3K4me3_WT_rep2"
+ "hg38.Lareau.hg38.full.Excludable"
  "hg38.Nordin.CandRblacklist_hg38"
  "ChIP_HL60_H3K4me3_WT_rep1"
  "HT1376_DMSO_H3K27me3"

    actual$metadata.genome_alias | expected$metadata.genome_alias    
[1] "hg19"                       - "hg38"                         [1]
[2] "hg38"                       - "hg19"                         [2]
[3] "hg19"                       | "hg19"                         [3]
[4] "hg38"                       | "hg38"                         [4]
[5] "hg38"                       - "hg19"                         [5]
[6] "hg19"                       - "hg38"                         [6]
[7] "hg38"                       | "hg38"                         [7]
[8] "hg19"                       | "hg19"                         [8]
[9] "hg38"                       | "hg38"                         [9]

    actual$metadata.bed_compliance | expected$metadata.bed_compliance    
[1] "bed6+4"                       - "bed4+3"                         [1]
[2] "bed4+3"                       - "bed6+4"                         [2]
[3] "bed6+4"                       | "bed6+4"                         [3]
[4] "bed4+7"                       | "bed4+7"                         [4]
[5] "bed4+1"                       - "bed6+4"                         [5]
[6] "bed6+4"                       - "bed4+1"                         [6]
[7] "bed4+1"                       | "bed4+1"                         [7]
[8] "bed6+4"                       | "bed6+4"                         [8]
[9] "bed3+0"                       | "bed3+0"                         [9]

    actual$metadata.data_format | expected$metadata.data_format    
[1] "encode_narrowpeak_rs"      - "bed_like"                    [1]
[2] "bed_like"                  - "encode_narrowpeak_rs"        [2]
[3] "encode_narrowpeak_rs"      | "encode_narrowpeak_rs"        [3]
[4] "bed_like"                  | "bed_like"                    [4]
[5] "bed_like"                  - "encode_narrowpeak_rs"        [5]
[6] "encode_narrowpeak_rs"      - "bed_like"                    [6]
[7] "bed_like"                  | "bed_like"                    [7]
[8] "encode_narrowpeak_rs"      | "encode_narrowpeak_rs"        [8]
[9] "ucsc_bed"                  | "ucsc_bed"                    [9]

`actual$metadata.compliant_columns[1:9]`:   "6" "4" "6" "4" "4" "6" "4" "6" "3"
`expected$metadata.compliant_columns[1:9]`: "4" "6" "6" "4" "6" "4" "4" "6" "3"

actual$metadata.non_compliant_columns[1:9] vs expected$metadata.non_compliant_columns[1:9]
- "4"
+ "3"
- "3"
+ "4"
  "4"
  "7"
- "1"
+ "4"
- "4"
+ "1"
  "1"
  "4"
  "0"

    actual$metadata.id                 | expected$metadata.id                  
[1] "6be4f1fb7464a8c2f68952755652d98b" - "2d86ffa3f593c74382caa04cd26130c5" [1]
[2] "2d86ffa3f593c74382caa04cd26130c5" - "6be4f1fb7464a8c2f68952755652d98b" [2]
[3] "3986a74ae4f05012f5c6e0be54877552" | "3986a74ae4f05012f5c6e0be54877552" [3]
[4] "3d80a48ef0b4a4ce69c48cacdc279242" | "3d80a48ef0b4a4ce69c48cacdc279242" [4]
[5] "388b4b726e760acf59974fd8aa83f1b7" - "5691d9009f96145641f0e3b9ff4f0735" [5]
[6] "5691d9009f96145641f0e3b9ff4f0735" - "388b4b726e760acf59974fd8aa83f1b7" [6]
[7] "2b93bec4ddad5fc2f30597257e7a0560" | "2b93bec4ddad5fc2f30597257e7a0560" [7]
[8] "1b7fc14e60f8affde442e6a061c55877" | "1b7fc14e60f8affde442e6a061c55877" [8]
[9] "9f17013256fca6c57227ba30abc0d99c" | "9f17013256fca6c57227ba30abc0d99c" [9]

actual$metadata.description[1:9] vs expected$metadata.description[1:9]
- ""
+ "Defined by the ENCODE consortium, includes satellite repeats (CATTC, GAATG, GAGTG, ACRO1), RepeatMasker repeats (ALR/Alpha, BSR/Beta), centromeric repeats, chrM, High/Low mappability islands. Has extra chromosomes, use keepStandardChromosomes() filtering"
- "Defined by the ENCODE consortium, includes satellite repeats (CATTC, GAATG, GAGTG, ACRO1), RepeatMasker repeats (ALR/Alpha, BSR/Beta), centromeric repeats, chrM, High/Low mappability islands. Has extra chromosomes, use keepStandardChromosomes() filtering"
+ ""
  ""
  "Gaps from large blocks of heterochromatin"
- "ENCODE excludable regions combined with regions of high homology to mtDNA (NUMT regions)"
+ ""
- ""
+ "ENCODE excludable regions combined with regions of high homology to mtDNA (NUMT regions)"
  "Defined from CUT&RUN negative controls as 0.1% top significant SEACR peaks in over 30% of samples"
  ""
  ""

    actual$metadata.submission_date | expected$metadata.submission_date    
[1] "2025-05-30T09:44:36.262173Z"   - "2025-05-05T18:28:58.015305Z"     [1]
[2] "2025-05-05T18:28:58.015305Z"   - "2025-05-30T09:44:36.262173Z"     [2]
[3] "2025-05-30T09:43:32.919054Z"   | "2025-05-30T09:43:32.919054Z"     [3]
[4] "2025-05-05T18:28:37.435229Z"   | "2025-05-05T18:28:37.435229Z"     [4]
[5] "2025-05-05T18:26:58.325651Z"   - "2025-05-30T09:46:40.540854Z"     [5]
[6] "2025-05-30T09:46:40.540854Z"   - "2025-05-05T18:26:58.325651Z"     [6]
[7] "2025-05-05T18:29:56.908488Z"   | "2025-05-05T18:29:56.908488Z"     [7]
[8] "2025-05-30T09:45:38.387577Z"   | "2025-05-30T09:45:38.387577Z"     [8]
[9] "2025-05-22T16:14:16.176590Z"   | "2025-05-22T16:14:16.176590Z"     [9]

    actual$metadata.last_update_date | expected$metadata.last_update_date    
[1] "2025-12-22T20:27:52.909252Z"    - "2025-12-23T02:03:22.366135Z"      [1]
[2] "2025-12-23T02:03:22.366135Z"    - "2025-12-22T20:27:52.909252Z"      [2]
[3] "2025-12-22T23:45:36.720524Z"    | "2025-12-22T23:45:36.720524Z"      [3]
[4] "2025-12-23T01:19:29.257195Z"    | "2025-12-23T01:19:29.257195Z"      [4]
[5] "2025-12-23T00:38:11.891694Z"    - "2025-12-23T02:01:27.110235Z"      [5]
[6] "2025-12-23T02:01:27.110235Z"    - "2025-12-23T00:38:11.891694Z"      [6]
[7] "2025-12-22T20:13:39.842611Z"    | "2025-12-22T20:13:39.842611Z"      [7]
[8] "2025-12-23T01:16:16.563707Z"    | "2025-12-23T01:16:16.563707Z"      [8]
[9] "2025-12-23T00:02:30.334754Z"    | "2025-12-23T00:02:30.334754Z"      [9]

actual$metadata.annotation.genotype[1:9] vs expected$metadata.annotation.genotype[1:9]
- "WT"
+ ""
- ""
+ "WT"
  "WT"
  ""
- ""
+ "WT"
- "WT"
+ ""
  ""
  "WT"
  ""

actual$metadata.annotation.cell_line[1:9] vs expected$metadata.annotation.cell_line[1:9]
- "HL-60"
+ ""
- ""
+ "HL-60"
  "HL-60"
  ""
- ""
+ "HL-60"
- "HL-60"
+ ""
  ""
  "HL-60"
  "HT1376"

actual$metadata.annotation.library_source[1:9] vs expected$metadata.annotation.library_source[1:9]
- "genomic"
+ ""
- ""
+ "genomic"
  "genomic"
  ""
- ""
+ "genomic"
- "genomic"
+ ""
  ""
  "genomic"
  "genomic"

    actual$metadata.annotation.assay | expected$metadata.annotation.assay    
[1] "ChIP-Seq"                       - ""                                 [1]
[2] ""                               - "ChIP-Seq"                         [2]
[3] "ChIP-Seq"                       | "ChIP-Seq"                         [3]
[4] ""                               | ""                                 [4]
[5] ""                               - "ChIP-Seq"                         [5]
[6] "ChIP-Seq"                       - ""                                 [6]
[7] ""                               | ""                                 [7]
[8] "ChIP-Seq"                       | "ChIP-Seq"                         [8]
[9] "ChIP-Seq"                       | "ChIP-Seq"                         [9]

actual$metadata.annotation.global_sample_id[1:9] vs expected$metadata.annotation.global_sample_id[1:9]
- "geo:gsm4378620"
+ "excluderanges:hg38.Reddy.wgEncodeDacMapabilityConsensusExcludable.hg38"
- "excluderanges:hg38.Reddy.wgEncodeDacMapabilityConsensusExcludable.hg38"
+ "geo:gsm4378620"
  "geo:gsm4378619"
  "excluderanges:hg38.UCSC.heterochromatin"
- "excluderanges:hg38.Lareau.hg38.full.Excludable"
+ "geo:gsm4378622"
- "geo:gsm4378622"
+ "excluderanges:hg38.Lareau.hg38.full.Excludable"
  "excluderanges:hg38.Nordin.CandRblacklist_hg38"
  "geo:gsm4378621"
  "geo:gsm5366300"

actual$metadata.annotation.global_experiment_id1[1:9] vs expected$metadata.annotation.global_experiment_id1[1:9]
- "geo:gse131577"
+ NA
- NA
+ "geo:gse131577"
  "geo:gse131577"
  NA
- NA
+ "geo:gse131577"
- "geo:gse131577"
+ NA
  NA
  "geo:gse131577"
  "geo:gse176486"

actual$metadata.annotation.global_experiment_id2[1:9] vs expected$metadata.annotation.global_experiment_id2[1:9]
- "geo:gse131583"
+ NA
- NA
+ "geo:gse131583"
  "geo:gse131583"
  NA
- NA
+ "geo:gse131583"
- "geo:gse131583"
+ NA
  NA
  "geo:gse131583"
  "geo:gse176493"

actual$metadata.annotation.original_file_name[1:9] vs expected$metadata.annotation.original_file_name[1:9]
- "GSM4378620_ChIP_HL60_H3K27ac_rep2_peaks.bed.gz"
+ "hg38.Reddy.wgEncodeDacMapabilityConsensusExcludable.hg38.bed"
- "hg38.Reddy.wgEncodeDacMapabilityConsensusExcludable.hg38.bed"
+ "GSM4378620_ChIP_HL60_H3K27ac_rep2_peaks.bed.gz"
  "GSM4378619_ChIP_HL60_H3K27ac_rep1_peaks.bed.gz"
  "hg38.UCSC.heterochromatin.bed"
- "hg38.Lareau.hg38.full.Excludable.bed"
+ "GSM4378622_ChIP_HL60_H3K4me3_rep2_peaks.bed.gz"
- "GSM4378622_ChIP_HL60_H3K4me3_rep2_peaks.bed.gz"
+ "hg38.Lareau.hg38.full.Excludable.bed"
  "hg38.Nordin.CandRblacklist_hg38.bed"
  "GSM4378621_ChIP_HL60_H3K4me3_rep1_peaks.bed.gz"
  "GSM5366300_H3K27me3-DMSO.bed.gz"

    actual$metadata.processed | expected$metadata.processed    
[2] "TRUE"                    | "TRUE"                      [2]
[3] "FALSE"                   | "FALSE"                     [3]
[4] "TRUE"                    | "TRUE"                      [4]
[5] "TRUE"                    - "FALSE"                     [5]
[6] "FALSE"                   - "TRUE"                      [6]
[7] "TRUE"                    | "TRUE"                      [7]
[8] "FALSE"                   | "FALSE"                     [8]
[9] "FALSE"                   | "FALSE"                     [9]

actual$payload.genome_digest[1:9] vs expected$payload.genome_digest[1:9]
- NA
+ "2230c535660fb4774114bfa966a62f823fdb6d21acf138d4"
- "2230c535660fb4774114bfa966a62f823fdb6d21acf138d4"
+ NA
  NA
  "2230c535660fb4774114bfa966a62f823fdb6d21acf138d4"
- "2230c535660fb4774114bfa966a62f823fdb6d21acf138d4"
+ NA
- NA
+ "2230c535660fb4774114bfa966a62f823fdb6d21acf138d4"
  "2230c535660fb4774114bfa966a62f823fdb6d21acf138d4"
  NA
  NA

actual$metadata.genome_digest[1:9] vs expected$metadata.genome_digest[1:9]
- NA
+ "2230c535660fb4774114bfa966a62f823fdb6d21acf138d4"
- "2230c535660fb4774114bfa966a62f823fdb6d21acf138d4"
+ NA
  NA
  "2230c535660fb4774114bfa966a62f823fdb6d21acf138d4"
- "2230c535660fb4774114bfa966a62f823fdb6d21acf138d4"
+ NA
- NA
+ "2230c535660fb4774114bfa966a62f823fdb6d21acf138d4"
  "2230c535660fb4774114bfa966a62f823fdb6d21acf138d4"
  NA
  NA

actual$metadata.annotation.global_experiment_id[1:9] vs expected$metadata.annotation.global_experiment_id[1:9]
- NA
+ "excluderanges"
- "excluderanges"
+ NA
  NA
  "excluderanges"
- "excluderanges"
+ NA
- NA
+ "excluderanges"
  "excluderanges"
  NA
  NA


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

Example timings

bedbaser.Rcheck/bedbaser-Ex.timings

name	user	system	elapsed
BEDbase	0.345	0.020	0.938
bb_bed_text_search	0.055	0.006	0.766
bb_beds_in_bedset	0.046	0.003	0.312
bb_example	0.058	0.004	0.355
bb_list_beds	0.104	0.006	0.533
bb_list_bedsets	0.120	0.006	4.924
bb_metadata	0.051	0.003	0.442
bb_save	0.093	0.025	1.890
bb_stats	0.033	0.002	0.347
bb_to_granges	6.249	0.445	7.783
bb_to_grangeslist	4.820	0.179	6.151
getCache-BEDbase-method	0.054	0.003	0.229
operations-BEDbase-method	0.035	0.004	0.215
schemas-BEDbase-method	0.033	0.002	0.202
setCache-BEDbase-method	0.044	0.004	0.229
tags-BEDbase-method	0.042	0.002	0.214