| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-01-06 11:35 -0500 (Tue, 06 Jan 2026).
| 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 | ||||
| Package 165/2332 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| bedbaser 1.3.0 (landing page) Andres Wokaty
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
|
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. |
| 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: 2026-01-05 18:37:31 -0500 (Mon, 05 Jan 2026) |
| EndedAt: 2026-01-05 18:39:06 -0500 (Mon, 05 Jan 2026) |
| EllapsedTime: 95.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: bedbaser.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### 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 5.437 0.389 6.792
bb_to_grangeslist 5.535 0.163 6.815
* 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:
+ "geo:gse131583"
NA
"geo:gse131583"
- NA
+ "geo:gse131583"
- "geo:gse131583"
+ NA
NA
"geo:gse176493"
[ 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.
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)
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/9/a/9ab5c0b7c51339314591b6017bdc41f5.bed.gz'
Content type 'binary/octet-stream' length 91823 bytes (89 KB)
==================================================
downloaded 89 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/8/1/8145c61d0d7a9cfacb50bac3c494889a.bed.gz'
Content type 'binary/octet-stream' length 357831 bytes (349 KB)
==================================================
downloaded 349 KB
trying URL 'https://api.bedbase.org/v1/files/files/0/5/054279c87e07890bb15a9462fceb7672.bed.gz'
Content type 'binary/octet-stream' length 246095 bytes (240 KB)
==================================================
downloaded 240 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/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/e/d/edf8211382727477eca95e8839faf157.bed.gz'
Content type 'binary/octet-stream' length 586392 bytes (572 KB)
==================================================
downloaded 572 KB
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:
actual vs expected
id payload.id payload.name payload.description payload.cell_line payload.assay payload.genome_alias payload.genome_digest metadata.name metadata.genome_alias metadata.genome_digest metadata.bed_compliance metadata.data_format metadata.compliant_columns metadata.non_compliant_columns metadata.id metadata.description metadata.submission_date metadata.last_update_date metadata.annotation.genotype metadata.annotation.cell_line metadata.annotation.library_source metadata.annotation.assay 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
actual[1, ] 2d86ffa3f593c74382caa04cd26130c5 2d86ffa3f593c74382caa04cd26130c5 hg38.Reddy.wgEncodeDacMapabilityConsensusExcludable.hg38 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 hg38 2230c535660fb4774114bfa966a62f823fdb6d21acf138d4 hg38.Reddy.wgEncodeDacMapabilityConsensusExcludable.hg38 hg38 2230c535660fb4774114bfa966a62f823fdb6d21acf138d4 bed4+3 bed_like 4 3 2d86ffa3f593c74382caa04cd26130c5 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 2025-05-05T18:28:58.015305Z 2025-12-23T02:03:22.366135Z excluderanges:hg38.Reddy.wgEncodeDacMapabilityConsensusExcludable.hg38 excluderanges hg38.Reddy.wgEncodeDacMapabilityConsensusExcludable.hg38.bed TRUE NA NA
actual[2, ] 6be4f1fb7464a8c2f68952755652d98b 6be4f1fb7464a8c2f68952755652d98b ChIP_HL60_H3K27ac_WT_rep2 HL-60 ChIP-Seq hg19 NA ChIP_HL60_H3K27ac_WT_rep2 hg19 NA bed6+4 encode_narrowpeak_rs 6 4 6be4f1fb7464a8c2f68952755652d98b 2025-05-30T09:44:36.262173Z 2025-12-22T20:27:52.909252Z WT HL-60 genomic ChIP-Seq geo:gsm4378620 NA GSM4378620_ChIP_HL60_H3K27ac_rep2_peaks.bed.gz TRUE geo:gse131577 geo:gse131583
- actual[3, ] 3986a74ae4f05012f5c6e0be54877552 3986a74ae4f05012f5c6e0be54877552 ChIP_HL60_H3K27ac_WT_rep1 HL-60 ChIP-Seq hg19 NA ChIP_HL60_H3K27ac_WT_rep1 hg19 NA bed6+4 encode_narrowpeak_rs 6 4 3986a74ae4f05012f5c6e0be54877552 2025-05-30T09:43:32.919054Z 2025-12-22T23:45:36.720524Z WT HL-60 genomic ChIP-Seq geo:gsm4378619 NA GSM4378619_ChIP_HL60_H3K27ac_rep1_peaks.bed.gz FALSE geo:gse131577 geo:gse131583
+ expected[3, ] 3d80a48ef0b4a4ce69c48cacdc279242 3d80a48ef0b4a4ce69c48cacdc279242 hg38.UCSC.heterochromatin Gaps from large blocks of heterochromatin hg38 2230c535660fb4774114bfa966a62f823fdb6d21acf138d4 hg38.UCSC.heterochromatin hg38 2230c535660fb4774114bfa966a62f823fdb6d21acf138d4 bed4+7 bed_like 4 7 3d80a48ef0b4a4ce69c48cacdc279242 Gaps from large blocks of heterochromatin 2025-05-05T18:28:37.435229Z 2025-12-23T01:19:29.257195Z excluderanges:hg38.UCSC.heterochromatin excluderanges hg38.UCSC.heterochromatin.bed TRUE NA NA
- actual[4, ] 3d80a48ef0b4a4ce69c48cacdc279242 3d80a48ef0b4a4ce69c48cacdc279242 hg38.UCSC.heterochromatin Gaps from large blocks of heterochromatin hg38 2230c535660fb4774114bfa966a62f823fdb6d21acf138d4 hg38.UCSC.heterochromatin hg38 2230c535660fb4774114bfa966a62f823fdb6d21acf138d4 bed4+7 bed_like 4 7 3d80a48ef0b4a4ce69c48cacdc279242 Gaps from large blocks of heterochromatin 2025-05-05T18:28:37.435229Z 2025-12-23T01:19:29.257195Z excluderanges:hg38.UCSC.heterochromatin excluderanges hg38.UCSC.heterochromatin.bed TRUE NA NA
+ expected[4, ] 3986a74ae4f05012f5c6e0be54877552 3986a74ae4f05012f5c6e0be54877552 ChIP_HL60_H3K27ac_WT_rep1 HL-60 ChIP-Seq hg19 NA ChIP_HL60_H3K27ac_WT_rep1 hg19 NA bed6+4 encode_narrowpeak_rs 6 4 3986a74ae4f05012f5c6e0be54877552 2025-05-30T09:43:32.919054Z 2025-12-22T23:45:36.720524Z WT HL-60 genomic ChIP-Seq geo:gsm4378619 NA GSM4378619_ChIP_HL60_H3K27ac_rep1_peaks.bed.gz FALSE geo:gse131577 geo:gse131583
actual[5, ] 388b4b726e760acf59974fd8aa83f1b7 388b4b726e760acf59974fd8aa83f1b7 hg38.Lareau.hg38.full.Excludable ENCODE excludable regions combined with regions of high homology to mtDNA (NUMT regions) hg38 2230c535660fb4774114bfa966a62f823fdb6d21acf138d4 hg38.Lareau.hg38.full.Excludable hg38 2230c535660fb4774114bfa966a62f823fdb6d21acf138d4 bed4+1 bed_like 4 1 388b4b726e760acf59974fd8aa83f1b7 ENCODE excludable regions combined with regions of high homology to mtDNA (NUMT regions) 2025-05-05T18:26:58.325651Z 2025-12-23T00:38:11.891694Z excluderanges:hg38.Lareau.hg38.full.Excludable excluderanges hg38.Lareau.hg38.full.Excludable.bed TRUE NA NA
actual[6, ] 5691d9009f96145641f0e3b9ff4f0735 5691d9009f96145641f0e3b9ff4f0735 ChIP_HL60_H3K4me3_WT_rep2 HL-60 ChIP-Seq hg19 NA ChIP_HL60_H3K4me3_WT_rep2 hg19 NA bed6+4 encode_narrowpeak_rs 6 4 5691d9009f96145641f0e3b9ff4f0735 2025-05-30T09:46:40.540854Z 2025-12-23T02:01:27.110235Z WT HL-60 genomic ChIP-Seq geo:gsm4378622 NA GSM4378622_ChIP_HL60_H3K4me3_rep2_peaks.bed.gz FALSE geo:gse131577 geo:gse131583
- actual[7, ] 2b93bec4ddad5fc2f30597257e7a0560 2b93bec4ddad5fc2f30597257e7a0560 hg38.Nordin.CandRblacklist_hg38 Defined from CUT&RUN negative controls as 0.1% top significant SEACR peaks in over 30% of samples hg38 2230c535660fb4774114bfa966a62f823fdb6d21acf138d4 hg38.Nordin.CandRblacklist_hg38 hg38 2230c535660fb4774114bfa966a62f823fdb6d21acf138d4 bed4+1 bed_like 4 1 2b93bec4ddad5fc2f30597257e7a0560 Defined from CUT&RUN negative controls as 0.1% top significant SEACR peaks in over 30% of samples 2025-05-05T18:29:56.908488Z 2025-12-22T20:13:39.842611Z excluderanges:hg38.Nordin.CandRblacklist_hg38 excluderanges hg38.Nordin.CandRblacklist_hg38.bed TRUE NA NA
+ expected[7, ] 1b7fc14e60f8affde442e6a061c55877 1b7fc14e60f8affde442e6a061c55877 ChIP_HL60_H3K4me3_WT_rep1 HL-60 ChIP-Seq hg19 NA ChIP_HL60_H3K4me3_WT_rep1 hg19 NA bed6+4 encode_narrowpeak_rs 6 4 1b7fc14e60f8affde442e6a061c55877 2025-05-30T09:45:38.387577Z 2025-12-23T01:16:16.563707Z WT HL-60 genomic ChIP-Seq geo:gsm4378621 NA GSM4378621_ChIP_HL60_H3K4me3_rep1_peaks.bed.gz FALSE geo:gse131577 geo:gse131583
- actual[8, ] 1b7fc14e60f8affde442e6a061c55877 1b7fc14e60f8affde442e6a061c55877 ChIP_HL60_H3K4me3_WT_rep1 HL-60 ChIP-Seq hg19 NA ChIP_HL60_H3K4me3_WT_rep1 hg19 NA bed6+4 encode_narrowpeak_rs 6 4 1b7fc14e60f8affde442e6a061c55877 2025-05-30T09:45:38.387577Z 2025-12-23T01:16:16.563707Z WT HL-60 genomic ChIP-Seq geo:gsm4378621 NA GSM4378621_ChIP_HL60_H3K4me3_rep1_peaks.bed.gz FALSE geo:gse131577 geo:gse131583
+ expected[8, ] 2b93bec4ddad5fc2f30597257e7a0560 2b93bec4ddad5fc2f30597257e7a0560 hg38.Nordin.CandRblacklist_hg38 Defined from CUT&RUN negative controls as 0.1% top significant SEACR peaks in over 30% of samples hg38 2230c535660fb4774114bfa966a62f823fdb6d21acf138d4 hg38.Nordin.CandRblacklist_hg38 hg38 2230c535660fb4774114bfa966a62f823fdb6d21acf138d4 bed4+1 bed_like 4 1 2b93bec4ddad5fc2f30597257e7a0560 Defined from CUT&RUN negative controls as 0.1% top significant SEACR peaks in over 30% of samples 2025-05-05T18:29:56.908488Z 2025-12-22T20:13:39.842611Z excluderanges:hg38.Nordin.CandRblacklist_hg38 excluderanges hg38.Nordin.CandRblacklist_hg38.bed TRUE NA NA
actual[9, ] 1f78a65cddf6a191599cd34ebf11201f 1f78a65cddf6a191599cd34ebf11201f hg38.Kundaje.GRCh38.Excludable Defined by Anshul Kundaje as a part of ENCODE and modENCODE consortia hg38 2230c535660fb4774114bfa966a62f823fdb6d21acf138d4 hg38.Kundaje.GRCh38.Excludable hg38 2230c535660fb4774114bfa966a62f823fdb6d21acf138d4 bed4+1 bed_like 4 1 1f78a65cddf6a191599cd34ebf11201f Defined by Anshul Kundaje as a part of ENCODE and modENCODE consortia 2025-05-05T18:26:48.498909Z 2025-12-22T20:29:29.690409Z excluderanges:hg38.Kundaje.GRCh38.Excludable excluderanges hg38.Kundaje.GRCh38.Excludable.bed TRUE NA NA
actual[10, ] 9f17013256fca6c57227ba30abc0d99c 9f17013256fca6c57227ba30abc0d99c HT1376_DMSO_H3K27me3 HT1376 ChIP-Seq hg38 NA HT1376_DMSO_H3K27me3 hg38 NA bed3+0 ucsc_bed 3 0 9f17013256fca6c57227ba30abc0d99c 2025-05-22T16:14:16.176590Z 2025-12-23T00:02:30.334754Z HT1376 genomic ChIP-Seq geo:gsm5366300 NA GSM5366300_H3K27me3-DMSO.bed.gz FALSE geo:gse176486 geo:gse176493
actual$id vs expected$id
"2d86ffa3f593c74382caa04cd26130c5"
"6be4f1fb7464a8c2f68952755652d98b"
- "3986a74ae4f05012f5c6e0be54877552"
+ "3d80a48ef0b4a4ce69c48cacdc279242"
- "3d80a48ef0b4a4ce69c48cacdc279242"
+ "3986a74ae4f05012f5c6e0be54877552"
"388b4b726e760acf59974fd8aa83f1b7"
"5691d9009f96145641f0e3b9ff4f0735"
- "2b93bec4ddad5fc2f30597257e7a0560"
+ "1b7fc14e60f8affde442e6a061c55877"
- "1b7fc14e60f8affde442e6a061c55877"
+ "2b93bec4ddad5fc2f30597257e7a0560"
"1f78a65cddf6a191599cd34ebf11201f"
"9f17013256fca6c57227ba30abc0d99c"
actual$payload.id vs expected$payload.id
"2d86ffa3f593c74382caa04cd26130c5"
"6be4f1fb7464a8c2f68952755652d98b"
- "3986a74ae4f05012f5c6e0be54877552"
+ "3d80a48ef0b4a4ce69c48cacdc279242"
- "3d80a48ef0b4a4ce69c48cacdc279242"
+ "3986a74ae4f05012f5c6e0be54877552"
"388b4b726e760acf59974fd8aa83f1b7"
"5691d9009f96145641f0e3b9ff4f0735"
- "2b93bec4ddad5fc2f30597257e7a0560"
+ "1b7fc14e60f8affde442e6a061c55877"
- "1b7fc14e60f8affde442e6a061c55877"
+ "2b93bec4ddad5fc2f30597257e7a0560"
"1f78a65cddf6a191599cd34ebf11201f"
"9f17013256fca6c57227ba30abc0d99c"
actual$payload.name vs expected$payload.name
"hg38.Reddy.wgEncodeDacMapabilityConsensusExcludable.hg38"
"ChIP_HL60_H3K27ac_WT_rep2"
- "ChIP_HL60_H3K27ac_WT_rep1"
+ "hg38.UCSC.heterochromatin"
- "hg38.UCSC.heterochromatin"
+ "ChIP_HL60_H3K27ac_WT_rep1"
"hg38.Lareau.hg38.full.Excludable"
"ChIP_HL60_H3K4me3_WT_rep2"
- "hg38.Nordin.CandRblacklist_hg38"
+ "ChIP_HL60_H3K4me3_WT_rep1"
- "ChIP_HL60_H3K4me3_WT_rep1"
+ "hg38.Nordin.CandRblacklist_hg38"
"hg38.Kundaje.GRCh38.Excludable"
"HT1376_DMSO_H3K27me3"
actual$payload.description vs expected$payload.description
"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"
- "Gaps from large blocks of heterochromatin"
+ ""
"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"
+ ""
- ""
+ "Defined from CUT&RUN negative controls as 0.1% top significant SEACR peaks in over 30% of samples"
"Defined by Anshul Kundaje as a part of ENCODE and modENCODE consortia"
""
actual$payload.cell_line | expected$payload.cell_line
[1] "" | "" [1]
[2] "HL-60" | "HL-60" [2]
[3] "HL-60" - "" [3]
[4] "" - "HL-60" [4]
[5] "" | "" [5]
[6] "HL-60" | "HL-60" [6]
[7] "" - "HL-60" [7]
[8] "HL-60" - "" [8]
[9] "" | "" [9]
[10] "HT1376" | "HT1376" [10]
actual$payload.assay | expected$payload.assay
[1] "" | "" [1]
[2] "ChIP-Seq" | "ChIP-Seq" [2]
[3] "ChIP-Seq" - "" [3]
[4] "" - "ChIP-Seq" [4]
[5] "" | "" [5]
[6] "ChIP-Seq" | "ChIP-Seq" [6]
[7] "" - "ChIP-Seq" [7]
[8] "ChIP-Seq" - "" [8]
[9] "" | "" [9]
[10] "ChIP-Seq" | "ChIP-Seq" [10]
actual$payload.genome_alias | expected$payload.genome_alias
[1] "hg38" | "hg38" [1]
[2] "hg19" | "hg19" [2]
[3] "hg19" - "hg38" [3]
[4] "hg38" - "hg19" [4]
[5] "hg38" | "hg38" [5]
[6] "hg19" | "hg19" [6]
[7] "hg38" - "hg19" [7]
[8] "hg19" - "hg38" [8]
[9] "hg38" | "hg38" [9]
[10] "hg38" | "hg38" [10]
actual$payload.genome_digest vs expected$payload.genome_digest
"2230c535660fb4774114bfa966a62f823fdb6d21acf138d4"
NA
- NA
+ "2230c535660fb4774114bfa966a62f823fdb6d21acf138d4"
- "2230c535660fb4774114bfa966a62f823fdb6d21acf138d4"
+ NA
"2230c535660fb4774114bfa966a62f823fdb6d21acf138d4"
NA
- "2230c535660fb4774114bfa966a62f823fdb6d21acf138d4"
+ NA
- NA
+ "2230c535660fb4774114bfa966a62f823fdb6d21acf138d4"
"2230c535660fb4774114bfa966a62f823fdb6d21acf138d4"
NA
actual$metadata.name vs expected$metadata.name
"hg38.Reddy.wgEncodeDacMapabilityConsensusExcludable.hg38"
"ChIP_HL60_H3K27ac_WT_rep2"
- "ChIP_HL60_H3K27ac_WT_rep1"
+ "hg38.UCSC.heterochromatin"
- "hg38.UCSC.heterochromatin"
+ "ChIP_HL60_H3K27ac_WT_rep1"
"hg38.Lareau.hg38.full.Excludable"
"ChIP_HL60_H3K4me3_WT_rep2"
- "hg38.Nordin.CandRblacklist_hg38"
+ "ChIP_HL60_H3K4me3_WT_rep1"
- "ChIP_HL60_H3K4me3_WT_rep1"
+ "hg38.Nordin.CandRblacklist_hg38"
"hg38.Kundaje.GRCh38.Excludable"
"HT1376_DMSO_H3K27me3"
actual$metadata.genome_alias | expected$metadata.genome_alias
[1] "hg38" | "hg38" [1]
[2] "hg19" | "hg19" [2]
[3] "hg19" - "hg38" [3]
[4] "hg38" - "hg19" [4]
[5] "hg38" | "hg38" [5]
[6] "hg19" | "hg19" [6]
[7] "hg38" - "hg19" [7]
[8] "hg19" - "hg38" [8]
[9] "hg38" | "hg38" [9]
[10] "hg38" | "hg38" [10]
actual$metadata.genome_digest vs expected$metadata.genome_digest
"2230c535660fb4774114bfa966a62f823fdb6d21acf138d4"
NA
- NA
+ "2230c535660fb4774114bfa966a62f823fdb6d21acf138d4"
- "2230c535660fb4774114bfa966a62f823fdb6d21acf138d4"
+ NA
"2230c535660fb4774114bfa966a62f823fdb6d21acf138d4"
NA
- "2230c535660fb4774114bfa966a62f823fdb6d21acf138d4"
+ NA
- NA
+ "2230c535660fb4774114bfa966a62f823fdb6d21acf138d4"
"2230c535660fb4774114bfa966a62f823fdb6d21acf138d4"
NA
actual$metadata.bed_compliance | expected$metadata.bed_compliance
[1] "bed4+3" | "bed4+3" [1]
[2] "bed6+4" | "bed6+4" [2]
[3] "bed6+4" - "bed4+7" [3]
[4] "bed4+7" - "bed6+4" [4]
[5] "bed4+1" | "bed4+1" [5]
[6] "bed6+4" | "bed6+4" [6]
[7] "bed4+1" - "bed6+4" [7]
[8] "bed6+4" - "bed4+1" [8]
[9] "bed4+1" | "bed4+1" [9]
[10] "bed3+0" | "bed3+0" [10]
actual$metadata.data_format | expected$metadata.data_format
[1] "bed_like" | "bed_like" [1]
[2] "encode_narrowpeak_rs" | "encode_narrowpeak_rs" [2]
[3] "encode_narrowpeak_rs" - "bed_like" [3]
[4] "bed_like" - "encode_narrowpeak_rs" [4]
[5] "bed_like" | "bed_like" [5]
[6] "encode_narrowpeak_rs" | "encode_narrowpeak_rs" [6]
[7] "bed_like" - "encode_narrowpeak_rs" [7]
[8] "encode_narrowpeak_rs" - "bed_like" [8]
[9] "bed_like" | "bed_like" [9]
[10] "ucsc_bed" | "ucsc_bed" [10]
`actual$metadata.compliant_columns`: "4" "6" "6" "4" "4" "6" "4" "6" "4" "3"
`expected$metadata.compliant_columns`: "4" "6" "4" "6" "4" "6" "6" "4" "4" "3"
actual$metadata.non_compliant_columns vs expected$metadata.non_compliant_columns
"3"
"4"
- "4"
+ "7"
- "7"
+ "4"
"1"
"4"
- "1"
+ "4"
- "4"
+ "1"
"1"
"0"
actual$metadata.id vs expected$metadata.id
"2d86ffa3f593c74382caa04cd26130c5"
"6be4f1fb7464a8c2f68952755652d98b"
- "3986a74ae4f05012f5c6e0be54877552"
+ "3d80a48ef0b4a4ce69c48cacdc279242"
- "3d80a48ef0b4a4ce69c48cacdc279242"
+ "3986a74ae4f05012f5c6e0be54877552"
"388b4b726e760acf59974fd8aa83f1b7"
"5691d9009f96145641f0e3b9ff4f0735"
- "2b93bec4ddad5fc2f30597257e7a0560"
+ "1b7fc14e60f8affde442e6a061c55877"
- "1b7fc14e60f8affde442e6a061c55877"
+ "2b93bec4ddad5fc2f30597257e7a0560"
"1f78a65cddf6a191599cd34ebf11201f"
"9f17013256fca6c57227ba30abc0d99c"
actual$metadata.description vs expected$metadata.description
"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"
- "Gaps from large blocks of heterochromatin"
+ ""
"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"
+ ""
- ""
+ "Defined from CUT&RUN negative controls as 0.1% top significant SEACR peaks in over 30% of samples"
"Defined by Anshul Kundaje as a part of ENCODE and modENCODE consortia"
""
actual$metadata.submission_date | expected$metadata.submission_date
[1] "2025-05-05T18:28:58.015305Z" | "2025-05-05T18:28:58.015305Z" [1]
[2] "2025-05-30T09:44:36.262173Z" | "2025-05-30T09:44:36.262173Z" [2]
[3] "2025-05-30T09:43:32.919054Z" - "2025-05-05T18:28:37.435229Z" [3]
[4] "2025-05-05T18:28:37.435229Z" - "2025-05-30T09:43:32.919054Z" [4]
[5] "2025-05-05T18:26:58.325651Z" | "2025-05-05T18:26:58.325651Z" [5]
[6] "2025-05-30T09:46:40.540854Z" | "2025-05-30T09:46:40.540854Z" [6]
[7] "2025-05-05T18:29:56.908488Z" - "2025-05-30T09:45:38.387577Z" [7]
[8] "2025-05-30T09:45:38.387577Z" - "2025-05-05T18:29:56.908488Z" [8]
[9] "2025-05-05T18:26:48.498909Z" | "2025-05-05T18:26:48.498909Z" [9]
[10] "2025-05-22T16:14:16.176590Z" | "2025-05-22T16:14:16.176590Z" [10]
actual$metadata.last_update_date | expected$metadata.last_update_date
[1] "2025-12-23T02:03:22.366135Z" | "2025-12-23T02:03:22.366135Z" [1]
[2] "2025-12-22T20:27:52.909252Z" | "2025-12-22T20:27:52.909252Z" [2]
[3] "2025-12-22T23:45:36.720524Z" - "2025-12-23T01:19:29.257195Z" [3]
[4] "2025-12-23T01:19:29.257195Z" - "2025-12-22T23:45:36.720524Z" [4]
[5] "2025-12-23T00:38:11.891694Z" | "2025-12-23T00:38:11.891694Z" [5]
[6] "2025-12-23T02:01:27.110235Z" | "2025-12-23T02:01:27.110235Z" [6]
[7] "2025-12-22T20:13:39.842611Z" - "2025-12-23T01:16:16.563707Z" [7]
[8] "2025-12-23T01:16:16.563707Z" - "2025-12-22T20:13:39.842611Z" [8]
[9] "2025-12-22T20:29:29.690409Z" | "2025-12-22T20:29:29.690409Z" [9]
[10] "2025-12-23T00:02:30.334754Z" | "2025-12-23T00:02:30.334754Z" [10]
actual$metadata.annotation.genotype vs expected$metadata.annotation.genotype
""
"WT"
- "WT"
+ ""
- ""
+ "WT"
""
"WT"
- ""
+ "WT"
- "WT"
+ ""
""
""
actual$metadata.annotation.cell_line vs expected$metadata.annotation.cell_line
""
"HL-60"
- "HL-60"
+ ""
- ""
+ "HL-60"
""
"HL-60"
- ""
+ "HL-60"
- "HL-60"
+ ""
""
"HT1376"
actual$metadata.annotation.library_source vs expected$metadata.annotation.library_source
""
"genomic"
- "genomic"
+ ""
- ""
+ "genomic"
""
"genomic"
- ""
+ "genomic"
- "genomic"
+ ""
""
"genomic"
actual$metadata.annotation.assay | expected$metadata.annotation.assay
[1] "" | "" [1]
[2] "ChIP-Seq" | "ChIP-Seq" [2]
[3] "ChIP-Seq" - "" [3]
[4] "" - "ChIP-Seq" [4]
[5] "" | "" [5]
[6] "ChIP-Seq" | "ChIP-Seq" [6]
[7] "" - "ChIP-Seq" [7]
[8] "ChIP-Seq" - "" [8]
[9] "" | "" [9]
[10] "ChIP-Seq" | "ChIP-Seq" [10]
actual$metadata.annotation.global_sample_id vs expected$metadata.annotation.global_sample_id
"excluderanges:hg38.Reddy.wgEncodeDacMapabilityConsensusExcludable.hg38"
"geo:gsm4378620"
- "geo:gsm4378619"
+ "excluderanges:hg38.UCSC.heterochromatin"
- "excluderanges:hg38.UCSC.heterochromatin"
+ "geo:gsm4378619"
"excluderanges:hg38.Lareau.hg38.full.Excludable"
"geo:gsm4378622"
- "excluderanges:hg38.Nordin.CandRblacklist_hg38"
+ "geo:gsm4378621"
- "geo:gsm4378621"
+ "excluderanges:hg38.Nordin.CandRblacklist_hg38"
"excluderanges:hg38.Kundaje.GRCh38.Excludable"
"geo:gsm5366300"
actual$metadata.annotation.global_experiment_id vs expected$metadata.annotation.global_experiment_id
"excluderanges"
NA
- NA
+ "excluderanges"
- "excluderanges"
+ NA
"excluderanges"
NA
- "excluderanges"
+ NA
- NA
+ "excluderanges"
"excluderanges"
NA
actual$metadata.annotation.original_file_name vs expected$metadata.annotation.original_file_name
"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.UCSC.heterochromatin.bed"
+ "GSM4378619_ChIP_HL60_H3K27ac_rep1_peaks.bed.gz"
"hg38.Lareau.hg38.full.Excludable.bed"
"GSM4378622_ChIP_HL60_H3K4me3_rep2_peaks.bed.gz"
- "hg38.Nordin.CandRblacklist_hg38.bed"
+ "GSM4378621_ChIP_HL60_H3K4me3_rep1_peaks.bed.gz"
- "GSM4378621_ChIP_HL60_H3K4me3_rep1_peaks.bed.gz"
+ "hg38.Nordin.CandRblacklist_hg38.bed"
"hg38.Kundaje.GRCh38.Excludable.bed"
"GSM5366300_H3K27me3-DMSO.bed.gz"
actual$metadata.processed | expected$metadata.processed
[1] "TRUE" | "TRUE" [1]
[2] "TRUE" | "TRUE" [2]
[3] "FALSE" - "TRUE" [3]
[4] "TRUE" - "FALSE" [4]
[5] "TRUE" | "TRUE" [5]
[6] "FALSE" | "FALSE" [6]
[7] "TRUE" - "FALSE" [7]
[8] "FALSE" - "TRUE" [8]
[9] "TRUE" | "TRUE" [9]
[10] "FALSE" | "FALSE" [10]
actual$metadata.annotation.global_experiment_id1 vs expected$metadata.annotation.global_experiment_id1
NA
"geo:gse131577"
- "geo:gse131577"
+ NA
- NA
+ "geo:gse131577"
NA
"geo:gse131577"
- NA
+ "geo:gse131577"
- "geo:gse131577"
+ NA
NA
"geo:gse176486"
actual$metadata.annotation.global_experiment_id2 vs expected$metadata.annotation.global_experiment_id2
NA
"geo:gse131583"
- "geo:gse131583"
+ NA
- NA
+ "geo:gse131583"
NA
"geo:gse131583"
- NA
+ "geo:gse131583"
- "geo:gse131583"
+ NA
NA
"geo:gse176493"
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 50 ]
Error:
! Test failures.
Execution halted
bedbaser.Rcheck/bedbaser-Ex.timings
| name | user | system | elapsed | |
| BEDbase | 0.359 | 0.018 | 0.930 | |
| bb_bed_text_search | 0.065 | 0.008 | 0.713 | |
| bb_beds_in_bedset | 0.051 | 0.003 | 0.304 | |
| bb_example | 0.069 | 0.005 | 0.356 | |
| bb_list_beds | 0.112 | 0.007 | 0.525 | |
| bb_list_bedsets | 0.127 | 0.007 | 4.605 | |
| bb_metadata | 0.053 | 0.003 | 0.726 | |
| bb_save | 0.066 | 0.010 | 1.550 | |
| bb_stats | 0.031 | 0.002 | 0.359 | |
| bb_to_granges | 5.437 | 0.389 | 6.792 | |
| bb_to_grangeslist | 5.535 | 0.163 | 6.815 | |
| getCache-BEDbase-method | 0.050 | 0.005 | 0.230 | |
| operations-BEDbase-method | 0.039 | 0.003 | 0.217 | |
| schemas-BEDbase-method | 0.029 | 0.002 | 0.212 | |
| setCache-BEDbase-method | 0.040 | 0.003 | 0.223 | |
| tags-BEDbase-method | 0.040 | 0.002 | 0.223 | |