| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-01-05 11:57 -0500 (Mon, 05 Jan 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4883 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4671 |
| 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 163/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| bedbaser 1.2.0 (landing page) Andres Wokaty
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
|
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: 1.2.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:bedbaser.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings bedbaser_1.2.0.tar.gz |
| StartedAt: 2026-01-01 21:19:38 -0500 (Thu, 01 Jan 2026) |
| EndedAt: 2026-01-01 21:23:56 -0500 (Thu, 01 Jan 2026) |
| EllapsedTime: 257.9 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: bedbaser.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:bedbaser.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings bedbaser_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/bedbaser.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 ‘1.2.0’
* 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 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 13.980 0.597 20.688
bb_to_granges 12.988 0.651 15.606
* 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:
+ "excluderanges"
- "excluderanges"
+ NA
- NA
+ "excluderanges"
- "excluderanges"
+ NA
"excluderanges"
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 re-building of vignette outputs ... OK
* 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.
bedbaser.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL bedbaser ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘bedbaser’ ... ** this is package ‘bedbaser’ version ‘1.2.0’ ** 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 version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
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")
Saving _problems/test-bedbaser-95.R
trying URL 'https://api.bedbase.org/v1/files/files/c/2/c2049dd886e4a40e4b18f7ef3fcec62e.bed.gz'
Content type 'binary/octet-stream' length 301004 bytes (293 KB)
==================================================
downloaded 293 KB
trying URL 'https://api.bedbase.org/v1/files/files/8/2/82cab3e0a2c9bcb32373898f591fda12.bed.gz'
Content type 'binary/octet-stream' length 459250 bytes (448 KB)
==================================================
downloaded 448 KB
trying URL 'https://api.bedbase.org/v1/files/files/e/a/eaa9cdb049514b4e298cd0f71f7e9be7.bed.gz'
Content type 'binary/octet-stream' length 1550728 bytes (1.5 MB)
==================================================
downloaded 1.5 MB
trying URL 'https://api.bedbase.org/v1/files/files/1/7/17b6ab3501850c675cc7963823fc6ee5.bed.gz'
Content type 'binary/octet-stream' length 676996 bytes (661 KB)
==================================================
downloaded 661 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/3/d/3dfea76224cbea014e99a78d7212a023.bed.gz'
Content type 'binary/octet-stream' length 5809492 bytes (5.5 MB)
==================================================
downloaded 5.5 MB
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 metadata.name metadata.genome_alias 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_id1 metadata.annotation.global_experiment_id2 metadata.annotation.original_file_name metadata.processed payload.genome_digest metadata.genome_digest metadata.annotation.global_experiment_id
actual[1, ] 6be4f1fb7464a8c2f68952755652d98b 6be4f1fb7464a8c2f68952755652d98b ChIP_HL60_H3K27ac_WT_rep2 HL-60 ChIP-Seq hg19 ChIP_HL60_H3K27ac_WT_rep2 hg19 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 geo:gse131577 geo:gse131583 GSM4378620_ChIP_HL60_H3K27ac_rep2_peaks.bed.gz TRUE NA NA NA
actual[2, ] 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 hg38.Reddy.wgEncodeDacMapabilityConsensusExcludable.hg38 hg38 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 NA NA hg38.Reddy.wgEncodeDacMapabilityConsensusExcludable.hg38.bed TRUE 2230c535660fb4774114bfa966a62f823fdb6d21acf138d4 2230c535660fb4774114bfa966a62f823fdb6d21acf138d4 excluderanges
- actual[3, ] 3d80a48ef0b4a4ce69c48cacdc279242 3d80a48ef0b4a4ce69c48cacdc279242 hg38.UCSC.heterochromatin Gaps from large blocks of heterochromatin hg38 hg38.UCSC.heterochromatin hg38 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 NA NA hg38.UCSC.heterochromatin.bed TRUE 2230c535660fb4774114bfa966a62f823fdb6d21acf138d4 2230c535660fb4774114bfa966a62f823fdb6d21acf138d4 excluderanges
+ expected[3, ] 3986a74ae4f05012f5c6e0be54877552 3986a74ae4f05012f5c6e0be54877552 ChIP_HL60_H3K27ac_WT_rep1 HL-60 ChIP-Seq hg19 ChIP_HL60_H3K27ac_WT_rep1 hg19 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 geo:gse131577 geo:gse131583 GSM4378619_ChIP_HL60_H3K27ac_rep1_peaks.bed.gz FALSE NA NA NA
- actual[4, ] 3986a74ae4f05012f5c6e0be54877552 3986a74ae4f05012f5c6e0be54877552 ChIP_HL60_H3K27ac_WT_rep1 HL-60 ChIP-Seq hg19 ChIP_HL60_H3K27ac_WT_rep1 hg19 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 geo:gse131577 geo:gse131583 GSM4378619_ChIP_HL60_H3K27ac_rep1_peaks.bed.gz FALSE NA NA NA
+ expected[4, ] 3d80a48ef0b4a4ce69c48cacdc279242 3d80a48ef0b4a4ce69c48cacdc279242 hg38.UCSC.heterochromatin Gaps from large blocks of heterochromatin hg38 hg38.UCSC.heterochromatin hg38 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 NA NA hg38.UCSC.heterochromatin.bed TRUE 2230c535660fb4774114bfa966a62f823fdb6d21acf138d4 2230c535660fb4774114bfa966a62f823fdb6d21acf138d4 excluderanges
- actual[5, ] 5691d9009f96145641f0e3b9ff4f0735 5691d9009f96145641f0e3b9ff4f0735 ChIP_HL60_H3K4me3_WT_rep2 HL-60 ChIP-Seq hg19 ChIP_HL60_H3K4me3_WT_rep2 hg19 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 geo:gse131577 geo:gse131583 GSM4378622_ChIP_HL60_H3K4me3_rep2_peaks.bed.gz FALSE NA NA NA
+ expected[5, ] 388b4b726e760acf59974fd8aa83f1b7 388b4b726e760acf59974fd8aa83f1b7 hg38.Lareau.hg38.full.Excludable ENCODE excludable regions combined with regions of high homology to mtDNA (NUMT regions) hg38 hg38.Lareau.hg38.full.Excludable hg38 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 NA NA hg38.Lareau.hg38.full.Excludable.bed TRUE 2230c535660fb4774114bfa966a62f823fdb6d21acf138d4 2230c535660fb4774114bfa966a62f823fdb6d21acf138d4 excluderanges
- actual[6, ] 388b4b726e760acf59974fd8aa83f1b7 388b4b726e760acf59974fd8aa83f1b7 hg38.Lareau.hg38.full.Excludable ENCODE excludable regions combined with regions of high homology to mtDNA (NUMT regions) hg38 hg38.Lareau.hg38.full.Excludable hg38 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 NA NA hg38.Lareau.hg38.full.Excludable.bed TRUE 2230c535660fb4774114bfa966a62f823fdb6d21acf138d4 2230c535660fb4774114bfa966a62f823fdb6d21acf138d4 excluderanges
+ expected[6, ] 5691d9009f96145641f0e3b9ff4f0735 5691d9009f96145641f0e3b9ff4f0735 ChIP_HL60_H3K4me3_WT_rep2 HL-60 ChIP-Seq hg19 ChIP_HL60_H3K4me3_WT_rep2 hg19 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 geo:gse131577 geo:gse131583 GSM4378622_ChIP_HL60_H3K4me3_rep2_peaks.bed.gz FALSE NA NA NA
- actual[7, ] 1b7fc14e60f8affde442e6a061c55877 1b7fc14e60f8affde442e6a061c55877 ChIP_HL60_H3K4me3_WT_rep1 HL-60 ChIP-Seq hg19 ChIP_HL60_H3K4me3_WT_rep1 hg19 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 geo:gse131577 geo:gse131583 GSM4378621_ChIP_HL60_H3K4me3_rep1_peaks.bed.gz FALSE NA NA NA
+ expected[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 hg38.Nordin.CandRblacklist_hg38 hg38 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 NA NA hg38.Nordin.CandRblacklist_hg38.bed TRUE 2230c535660fb4774114bfa966a62f823fdb6d21acf138d4 2230c535660fb4774114bfa966a62f823fdb6d21acf138d4 excluderanges
- actual[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 hg38.Nordin.CandRblacklist_hg38 hg38 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 NA NA hg38.Nordin.CandRblacklist_hg38.bed TRUE 2230c535660fb4774114bfa966a62f823fdb6d21acf138d4 2230c535660fb4774114bfa966a62f823fdb6d21acf138d4 excluderanges
+ expected[8, ] 1b7fc14e60f8affde442e6a061c55877 1b7fc14e60f8affde442e6a061c55877 ChIP_HL60_H3K4me3_WT_rep1 HL-60 ChIP-Seq hg19 ChIP_HL60_H3K4me3_WT_rep1 hg19 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 geo:gse131577 geo:gse131583 GSM4378621_ChIP_HL60_H3K4me3_rep1_peaks.bed.gz FALSE NA NA NA
actual[9, ] 1f78a65cddf6a191599cd34ebf11201f 1f78a65cddf6a191599cd34ebf11201f hg38.Kundaje.GRCh38.Excludable Defined by Anshul Kundaje as a part of ENCODE and modENCODE consortia hg38 hg38.Kundaje.GRCh38.Excludable hg38 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 NA NA hg38.Kundaje.GRCh38.Excludable.bed TRUE 2230c535660fb4774114bfa966a62f823fdb6d21acf138d4 2230c535660fb4774114bfa966a62f823fdb6d21acf138d4 excluderanges
actual[10, ] 9f17013256fca6c57227ba30abc0d99c 9f17013256fca6c57227ba30abc0d99c HT1376_DMSO_H3K27me3 HT1376 ChIP-Seq hg38 HT1376_DMSO_H3K27me3 hg38 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 geo:gse176486 geo:gse176493 GSM5366300_H3K27me3-DMSO.bed.gz FALSE NA NA NA
actual$id vs expected$id
"6be4f1fb7464a8c2f68952755652d98b"
"2d86ffa3f593c74382caa04cd26130c5"
- "3d80a48ef0b4a4ce69c48cacdc279242"
+ "3986a74ae4f05012f5c6e0be54877552"
- "3986a74ae4f05012f5c6e0be54877552"
+ "3d80a48ef0b4a4ce69c48cacdc279242"
- "5691d9009f96145641f0e3b9ff4f0735"
+ "388b4b726e760acf59974fd8aa83f1b7"
- "388b4b726e760acf59974fd8aa83f1b7"
+ "5691d9009f96145641f0e3b9ff4f0735"
- "1b7fc14e60f8affde442e6a061c55877"
+ "2b93bec4ddad5fc2f30597257e7a0560"
- "2b93bec4ddad5fc2f30597257e7a0560"
+ "1b7fc14e60f8affde442e6a061c55877"
"1f78a65cddf6a191599cd34ebf11201f"
"9f17013256fca6c57227ba30abc0d99c"
actual$payload.id vs expected$payload.id
"6be4f1fb7464a8c2f68952755652d98b"
"2d86ffa3f593c74382caa04cd26130c5"
- "3d80a48ef0b4a4ce69c48cacdc279242"
+ "3986a74ae4f05012f5c6e0be54877552"
- "3986a74ae4f05012f5c6e0be54877552"
+ "3d80a48ef0b4a4ce69c48cacdc279242"
- "5691d9009f96145641f0e3b9ff4f0735"
+ "388b4b726e760acf59974fd8aa83f1b7"
- "388b4b726e760acf59974fd8aa83f1b7"
+ "5691d9009f96145641f0e3b9ff4f0735"
- "1b7fc14e60f8affde442e6a061c55877"
+ "2b93bec4ddad5fc2f30597257e7a0560"
- "2b93bec4ddad5fc2f30597257e7a0560"
+ "1b7fc14e60f8affde442e6a061c55877"
"1f78a65cddf6a191599cd34ebf11201f"
"9f17013256fca6c57227ba30abc0d99c"
actual$payload.name vs expected$payload.name
"ChIP_HL60_H3K27ac_WT_rep2"
"hg38.Reddy.wgEncodeDacMapabilityConsensusExcludable.hg38"
- "hg38.UCSC.heterochromatin"
+ "ChIP_HL60_H3K27ac_WT_rep1"
- "ChIP_HL60_H3K27ac_WT_rep1"
+ "hg38.UCSC.heterochromatin"
- "ChIP_HL60_H3K4me3_WT_rep2"
+ "hg38.Lareau.hg38.full.Excludable"
- "hg38.Lareau.hg38.full.Excludable"
+ "ChIP_HL60_H3K4me3_WT_rep2"
- "ChIP_HL60_H3K4me3_WT_rep1"
+ "hg38.Nordin.CandRblacklist_hg38"
- "hg38.Nordin.CandRblacklist_hg38"
+ "ChIP_HL60_H3K4me3_WT_rep1"
"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)"
- "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] "HL-60" | "HL-60" [1]
[2] "" | "" [2]
[3] "" - "HL-60" [3]
[4] "HL-60" - "" [4]
[5] "HL-60" - "" [5]
[6] "" - "HL-60" [6]
[7] "HL-60" - "" [7]
[8] "" - "HL-60" [8]
[9] "" | "" [9]
[10] "HT1376" | "HT1376" [10]
actual$payload.assay | expected$payload.assay
[1] "ChIP-Seq" | "ChIP-Seq" [1]
[2] "" | "" [2]
[3] "" - "ChIP-Seq" [3]
[4] "ChIP-Seq" - "" [4]
[5] "ChIP-Seq" - "" [5]
[6] "" - "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] "hg19" | "hg19" [1]
[2] "hg38" | "hg38" [2]
[3] "hg38" - "hg19" [3]
[4] "hg19" - "hg38" [4]
[5] "hg19" - "hg38" [5]
[6] "hg38" - "hg19" [6]
[7] "hg19" - "hg38" [7]
[8] "hg38" - "hg19" [8]
[9] "hg38" | "hg38" [9]
[10] "hg38" | "hg38" [10]
actual$metadata.name vs expected$metadata.name
"ChIP_HL60_H3K27ac_WT_rep2"
"hg38.Reddy.wgEncodeDacMapabilityConsensusExcludable.hg38"
- "hg38.UCSC.heterochromatin"
+ "ChIP_HL60_H3K27ac_WT_rep1"
- "ChIP_HL60_H3K27ac_WT_rep1"
+ "hg38.UCSC.heterochromatin"
- "ChIP_HL60_H3K4me3_WT_rep2"
+ "hg38.Lareau.hg38.full.Excludable"
- "hg38.Lareau.hg38.full.Excludable"
+ "ChIP_HL60_H3K4me3_WT_rep2"
- "ChIP_HL60_H3K4me3_WT_rep1"
+ "hg38.Nordin.CandRblacklist_hg38"
- "hg38.Nordin.CandRblacklist_hg38"
+ "ChIP_HL60_H3K4me3_WT_rep1"
"hg38.Kundaje.GRCh38.Excludable"
"HT1376_DMSO_H3K27me3"
actual$metadata.genome_alias | expected$metadata.genome_alias
[1] "hg19" | "hg19" [1]
[2] "hg38" | "hg38" [2]
[3] "hg38" - "hg19" [3]
[4] "hg19" - "hg38" [4]
[5] "hg19" - "hg38" [5]
[6] "hg38" - "hg19" [6]
[7] "hg19" - "hg38" [7]
[8] "hg38" - "hg19" [8]
[9] "hg38" | "hg38" [9]
[10] "hg38" | "hg38" [10]
actual$metadata.bed_compliance | expected$metadata.bed_compliance
[1] "bed6+4" | "bed6+4" [1]
[2] "bed4+3" | "bed4+3" [2]
[3] "bed4+7" - "bed6+4" [3]
[4] "bed6+4" - "bed4+7" [4]
[5] "bed6+4" - "bed4+1" [5]
[6] "bed4+1" - "bed6+4" [6]
[7] "bed6+4" - "bed4+1" [7]
[8] "bed4+1" - "bed6+4" [8]
[9] "bed4+1" | "bed4+1" [9]
[10] "bed3+0" | "bed3+0" [10]
actual$metadata.data_format | expected$metadata.data_format
[1] "encode_narrowpeak_rs" | "encode_narrowpeak_rs" [1]
[2] "bed_like" | "bed_like" [2]
[3] "bed_like" - "encode_narrowpeak_rs" [3]
[4] "encode_narrowpeak_rs" - "bed_like" [4]
[5] "encode_narrowpeak_rs" - "bed_like" [5]
[6] "bed_like" - "encode_narrowpeak_rs" [6]
[7] "encode_narrowpeak_rs" - "bed_like" [7]
[8] "bed_like" - "encode_narrowpeak_rs" [8]
[9] "bed_like" | "bed_like" [9]
[10] "ucsc_bed" | "ucsc_bed" [10]
`actual$metadata.compliant_columns`: "6" "4" "4" "6" "6" "4" "6" "4" "4" "3"
`expected$metadata.compliant_columns`: "6" "4" "6" "4" "4" "6" "4" "6" "4" "3"
actual$metadata.non_compliant_columns vs expected$metadata.non_compliant_columns
"4"
"3"
- "7"
+ "4"
- "4"
+ "7"
- "4"
+ "1"
- "1"
+ "4"
- "4"
+ "1"
- "1"
+ "4"
"1"
"0"
actual$metadata.id vs expected$metadata.id
"6be4f1fb7464a8c2f68952755652d98b"
"2d86ffa3f593c74382caa04cd26130c5"
- "3d80a48ef0b4a4ce69c48cacdc279242"
+ "3986a74ae4f05012f5c6e0be54877552"
- "3986a74ae4f05012f5c6e0be54877552"
+ "3d80a48ef0b4a4ce69c48cacdc279242"
- "5691d9009f96145641f0e3b9ff4f0735"
+ "388b4b726e760acf59974fd8aa83f1b7"
- "388b4b726e760acf59974fd8aa83f1b7"
+ "5691d9009f96145641f0e3b9ff4f0735"
- "1b7fc14e60f8affde442e6a061c55877"
+ "2b93bec4ddad5fc2f30597257e7a0560"
- "2b93bec4ddad5fc2f30597257e7a0560"
+ "1b7fc14e60f8affde442e6a061c55877"
"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)"
- "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] "2025-05-30T09:44:36.262173Z" | "2025-05-30T09:44:36.262173Z" [1]
[2] "2025-05-05T18:28:58.015305Z" | "2025-05-05T18:28:58.015305Z" [2]
[3] "2025-05-05T18:28:37.435229Z" - "2025-05-30T09:43:32.919054Z" [3]
[4] "2025-05-30T09:43:32.919054Z" - "2025-05-05T18:28:37.435229Z" [4]
[5] "2025-05-30T09:46:40.540854Z" - "2025-05-05T18:26:58.325651Z" [5]
[6] "2025-05-05T18:26:58.325651Z" - "2025-05-30T09:46:40.540854Z" [6]
[7] "2025-05-30T09:45:38.387577Z" - "2025-05-05T18:29:56.908488Z" [7]
[8] "2025-05-05T18:29:56.908488Z" - "2025-05-30T09:45:38.387577Z" [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] "2025-12-22T20:27:52.909252Z" | "2025-12-22T20:27:52.909252Z" [1]
[2] "2025-12-23T02:03:22.366135Z" | "2025-12-23T02:03:22.366135Z" [2]
[3] "2025-12-23T01:19:29.257195Z" - "2025-12-22T23:45:36.720524Z" [3]
[4] "2025-12-22T23:45:36.720524Z" - "2025-12-23T01:19:29.257195Z" [4]
[5] "2025-12-23T02:01:27.110235Z" - "2025-12-23T00:38:11.891694Z" [5]
[6] "2025-12-23T00:38:11.891694Z" - "2025-12-23T02:01:27.110235Z" [6]
[7] "2025-12-23T01:16:16.563707Z" - "2025-12-22T20:13:39.842611Z" [7]
[8] "2025-12-22T20:13:39.842611Z" - "2025-12-23T01:16:16.563707Z" [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"
+ ""
- ""
+ "WT"
""
""
actual$metadata.annotation.cell_line vs expected$metadata.annotation.cell_line
"HL-60"
""
- ""
+ "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"
""
"genomic"
actual$metadata.annotation.assay | expected$metadata.annotation.assay
[1] "ChIP-Seq" | "ChIP-Seq" [1]
[2] "" | "" [2]
[3] "" - "ChIP-Seq" [3]
[4] "ChIP-Seq" - "" [4]
[5] "ChIP-Seq" - "" [5]
[6] "" - "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
"geo:gsm4378620"
"excluderanges:hg38.Reddy.wgEncodeDacMapabilityConsensusExcludable.hg38"
- "excluderanges:hg38.UCSC.heterochromatin"
+ "geo:gsm4378619"
- "geo:gsm4378619"
+ "excluderanges:hg38.UCSC.heterochromatin"
- "geo:gsm4378622"
+ "excluderanges:hg38.Lareau.hg38.full.Excludable"
- "excluderanges:hg38.Lareau.hg38.full.Excludable"
+ "geo:gsm4378622"
- "geo:gsm4378621"
+ "excluderanges:hg38.Nordin.CandRblacklist_hg38"
- "excluderanges:hg38.Nordin.CandRblacklist_hg38"
+ "geo:gsm4378621"
"excluderanges:hg38.Kundaje.GRCh38.Excludable"
"geo:gsm5366300"
actual$metadata.annotation.global_experiment_id1 vs expected$metadata.annotation.global_experiment_id1
"geo:gse131577"
NA
- NA
+ "geo:gse131577"
- "geo:gse131577"
+ NA
- "geo:gse131577"
+ NA
- NA
+ "geo:gse131577"
- "geo:gse131577"
+ NA
- NA
+ "geo:gse131577"
NA
"geo:gse176486"
actual$metadata.annotation.global_experiment_id2 vs expected$metadata.annotation.global_experiment_id2
"geo:gse131583"
NA
- NA
+ "geo:gse131583"
- "geo:gse131583"
+ NA
- "geo:gse131583"
+ NA
- NA
+ "geo:gse131583"
- "geo:gse131583"
+ NA
- NA
+ "geo:gse131583"
NA
"geo:gse176493"
actual$metadata.annotation.original_file_name vs expected$metadata.annotation.original_file_name
"GSM4378620_ChIP_HL60_H3K27ac_rep2_peaks.bed.gz"
"hg38.Reddy.wgEncodeDacMapabilityConsensusExcludable.hg38.bed"
- "hg38.UCSC.heterochromatin.bed"
+ "GSM4378619_ChIP_HL60_H3K27ac_rep1_peaks.bed.gz"
- "GSM4378619_ChIP_HL60_H3K27ac_rep1_peaks.bed.gz"
+ "hg38.UCSC.heterochromatin.bed"
- "GSM4378622_ChIP_HL60_H3K4me3_rep2_peaks.bed.gz"
+ "hg38.Lareau.hg38.full.Excludable.bed"
- "hg38.Lareau.hg38.full.Excludable.bed"
+ "GSM4378622_ChIP_HL60_H3K4me3_rep2_peaks.bed.gz"
- "GSM4378621_ChIP_HL60_H3K4me3_rep1_peaks.bed.gz"
+ "hg38.Nordin.CandRblacklist_hg38.bed"
- "hg38.Nordin.CandRblacklist_hg38.bed"
+ "GSM4378621_ChIP_HL60_H3K4me3_rep1_peaks.bed.gz"
"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] "TRUE" - "FALSE" [3]
[4] "FALSE" - "TRUE" [4]
[5] "FALSE" - "TRUE" [5]
[6] "TRUE" - "FALSE" [6]
[7] "FALSE" - "TRUE" [7]
[8] "TRUE" - "FALSE" [8]
[9] "TRUE" | "TRUE" [9]
[10] "FALSE" | "FALSE" [10]
actual$payload.genome_digest vs expected$payload.genome_digest
NA
"2230c535660fb4774114bfa966a62f823fdb6d21acf138d4"
- "2230c535660fb4774114bfa966a62f823fdb6d21acf138d4"
+ NA
- NA
+ "2230c535660fb4774114bfa966a62f823fdb6d21acf138d4"
- NA
+ "2230c535660fb4774114bfa966a62f823fdb6d21acf138d4"
- "2230c535660fb4774114bfa966a62f823fdb6d21acf138d4"
+ NA
- NA
+ "2230c535660fb4774114bfa966a62f823fdb6d21acf138d4"
- "2230c535660fb4774114bfa966a62f823fdb6d21acf138d4"
+ NA
"2230c535660fb4774114bfa966a62f823fdb6d21acf138d4"
NA
actual$metadata.genome_digest vs expected$metadata.genome_digest
NA
"2230c535660fb4774114bfa966a62f823fdb6d21acf138d4"
- "2230c535660fb4774114bfa966a62f823fdb6d21acf138d4"
+ NA
- NA
+ "2230c535660fb4774114bfa966a62f823fdb6d21acf138d4"
- NA
+ "2230c535660fb4774114bfa966a62f823fdb6d21acf138d4"
- "2230c535660fb4774114bfa966a62f823fdb6d21acf138d4"
+ NA
- NA
+ "2230c535660fb4774114bfa966a62f823fdb6d21acf138d4"
- "2230c535660fb4774114bfa966a62f823fdb6d21acf138d4"
+ NA
"2230c535660fb4774114bfa966a62f823fdb6d21acf138d4"
NA
actual$metadata.annotation.global_experiment_id vs expected$metadata.annotation.global_experiment_id
NA
"excluderanges"
- "excluderanges"
+ NA
- NA
+ "excluderanges"
- NA
+ "excluderanges"
- "excluderanges"
+ NA
- NA
+ "excluderanges"
- "excluderanges"
+ NA
"excluderanges"
NA
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 50 ]
Error:
! Test failures.
Execution halted
bedbaser.Rcheck/bedbaser-Ex.timings
| name | user | system | elapsed | |
| BEDbase | 0.888 | 0.041 | 1.425 | |
| bb_bed_text_search | 0.166 | 0.029 | 0.852 | |
| bb_beds_in_bedset | 0.142 | 0.002 | 0.498 | |
| bb_example | 0.155 | 0.003 | 0.524 | |
| bb_list_beds | 0.309 | 0.013 | 0.849 | |
| bb_list_bedsets | 0.328 | 0.010 | 4.805 | |
| bb_metadata | 0.203 | 0.003 | 0.764 | |
| bb_save | 0.384 | 0.022 | 1.995 | |
| bb_stats | 0.100 | 0.003 | 0.487 | |
| bb_to_granges | 12.988 | 0.651 | 15.606 | |
| bb_to_grangeslist | 13.980 | 0.597 | 20.688 | |
| getCache-BEDbase-method | 0.140 | 0.002 | 0.372 | |
| operations-BEDbase-method | 0.094 | 0.003 | 0.317 | |
| schemas-BEDbase-method | 0.115 | 0.002 | 0.340 | |
| setCache-BEDbase-method | 0.115 | 0.003 | 0.338 | |
| tags-BEDbase-method | 0.119 | 0.001 | 0.342 | |