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This page was generated on 2025-10-16 11:37 -0400 (Thu, 16 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.6 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.7.5 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4586
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 343/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPpeakAnno 3.42.0  (landing page)
Jianhong Ou
Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025)
git_url: https://git.bioconductor.org/packages/ChIPpeakAnno
git_branch: RELEASE_3_21
git_last_commit: 6a1e893
git_last_commit_date: 2025-04-15 09:45:26 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.7.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    TIMEOUT  


CHECK results for ChIPpeakAnno on nebbiolo1

To the developers/maintainers of the ChIPpeakAnno package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ChIPpeakAnno.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: ChIPpeakAnno
Version: 3.42.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings ChIPpeakAnno_3.42.0.tar.gz
StartedAt: 2025-10-15 21:41:10 -0400 (Wed, 15 Oct 2025)
EndedAt: 2025-10-15 22:06:02 -0400 (Wed, 15 Oct 2025)
EllapsedTime: 1492.0 seconds
RetCode: 0
Status:   OK  
CheckDir: ChIPpeakAnno.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings ChIPpeakAnno_3.42.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/ChIPpeakAnno.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘ChIPpeakAnno/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChIPpeakAnno’ version ‘3.42.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 29 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘ChIPpeakAnno’ can be installed ... OK
* checking installed package size ... INFO
  installed size is 19.1Mb
  sub-directories of 1Mb or more:
    data     12.6Mb
    extdata   5.2Mb
* 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 ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
findEnhancers            22.947  0.839  23.793
findMotifsInPromoterSeqs 13.939  0.525  14.465
annotatePeakInBatch      11.855  1.090  12.950
summarizeOverlapsByBins   5.792  0.551   6.058
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* 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: OK


Installation output

ChIPpeakAnno.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL ChIPpeakAnno
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘ChIPpeakAnno’ ...
** this is package ‘ChIPpeakAnno’ version ‘3.42.0’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** 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 (ChIPpeakAnno)

Tests output

ChIPpeakAnno.Rcheck/tests/runTests.Rout


R version 4.5.1 (2025-06-13) -- "Great Square Root"
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.

> require("ChIPpeakAnno") || stop("unable to load Package:ChIPpeakAnno")
Loading required package: ChIPpeakAnno
Loading required package: IRanges
Loading required package: BiocGenerics
Loading required package: generics

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

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    findMatches

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

    I, expand.grid, unname

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
[1] TRUE
> require("BSgenome.Drerio.UCSC.danRer7") || stop("unable to load Package:BSgenome.Drerio.UCSC.danRer7")
Loading required package: BSgenome.Drerio.UCSC.danRer7
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: BiocIO
Loading required package: rtracklayer
[1] TRUE
> require("BSgenome.Hsapiens.UCSC.hg19") || stop("unable to load Package:BSgenome.Hsapiens.UCSC.hg19")
Loading required package: BSgenome.Hsapiens.UCSC.hg19
[1] TRUE
> require("org.Hs.eg.db") || stop("unable to load Package:org.Hs.eg.db")
Loading required package: org.Hs.eg.db
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


[1] TRUE
> require("org.Ce.eg.db") || stop("unable to load Package:org.Ce.eg.db")
Loading required package: org.Ce.eg.db

[1] TRUE
> require("BSgenome.Celegans.UCSC.ce10") || stop("unable to load Package:BSgenome.Celegans.UCSC.ce10")
Loading required package: BSgenome.Celegans.UCSC.ce10
[1] TRUE
> require("EnsDb.Hsapiens.v79") || stop("unable to load Package:EnsDb.Hsapiens.v79")
Loading required package: EnsDb.Hsapiens.v79
Loading required package: ensembldb
Loading required package: GenomicFeatures
Loading required package: AnnotationFilter

Attaching package: 'ensembldb'

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

    filter

[1] TRUE
> require("TxDb.Hsapiens.UCSC.hg38.knownGene") || stop("unable to load TxDb.Hsapiens.UCSC.hg38.knownGene")
Loading required package: TxDb.Hsapiens.UCSC.hg38.knownGene
[1] TRUE
> require("biomaRt") || stop("unable to load biomaRt")
Loading required package: biomaRt
[1] TRUE
> require("reactome.db") || stop("unable to load reactome.db")
Loading required package: reactome.db
[1] TRUE
> require("testthat") || stop("unable to load testthat")
Loading required package: testthat

Attaching package: 'testthat'

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

    not

[1] TRUE
> test_check("ChIPpeakAnno")
INFO [2025-10-15 21:50:57] $cat.cex
INFO [2025-10-15 21:50:57] [1] 1
INFO [2025-10-15 21:50:57] 
INFO [2025-10-15 21:50:57] $cat.col
INFO [2025-10-15 21:50:57] [1] "black"
INFO [2025-10-15 21:50:57] 
INFO [2025-10-15 21:50:57] $cat.fontface
INFO [2025-10-15 21:50:57] [1] "plain"
INFO [2025-10-15 21:50:57] 
INFO [2025-10-15 21:50:57] $cat.fontfamily
INFO [2025-10-15 21:50:57] [1] "serif"
INFO [2025-10-15 21:50:57] 
INFO [2025-10-15 21:50:57] $x
INFO [2025-10-15 21:50:57] $x$TF1
INFO [2025-10-15 21:50:57] [1] 3 4 5
INFO [2025-10-15 21:50:57] 
INFO [2025-10-15 21:50:57] $x$TF2
INFO [2025-10-15 21:50:57] [1] 1 2 3 4 5
INFO [2025-10-15 21:50:57] 
INFO [2025-10-15 21:50:57] 
INFO [2025-10-15 21:50:57] $disable.logging
INFO [2025-10-15 21:50:57] [1] TRUE
INFO [2025-10-15 21:50:57] 
INFO [2025-10-15 21:50:57] $filename
INFO [2025-10-15 21:50:57] NULL
INFO [2025-10-15 21:50:57] 
INFO [2025-10-15 21:50:58] $cat.cex
INFO [2025-10-15 21:50:58] [1] 1
INFO [2025-10-15 21:50:58] 
INFO [2025-10-15 21:50:58] $cat.col
INFO [2025-10-15 21:50:58] [1] "black"
INFO [2025-10-15 21:50:58] 
INFO [2025-10-15 21:50:58] $cat.fontface
INFO [2025-10-15 21:50:58] [1] "plain"
INFO [2025-10-15 21:50:58] 
INFO [2025-10-15 21:50:58] $cat.fontfamily
INFO [2025-10-15 21:50:58] [1] "serif"
INFO [2025-10-15 21:50:58] 
INFO [2025-10-15 21:50:58] $x
INFO [2025-10-15 21:50:58] $x$TF1
INFO [2025-10-15 21:50:58] [1] 3 4 5
INFO [2025-10-15 21:50:58] 
INFO [2025-10-15 21:50:58] $x$TF2
INFO [2025-10-15 21:50:58] [1] 1 2 4 5
INFO [2025-10-15 21:50:58] 
INFO [2025-10-15 21:50:58] $x$TF3
INFO [2025-10-15 21:50:58] [1] 3 4 5
INFO [2025-10-15 21:50:58] 
INFO [2025-10-15 21:50:58] $x$TF4
INFO [2025-10-15 21:50:58] [1] 1 2 4 5
INFO [2025-10-15 21:50:58] 
INFO [2025-10-15 21:50:58] 
INFO [2025-10-15 21:50:58] $disable.logging
INFO [2025-10-15 21:50:58] [1] TRUE
INFO [2025-10-15 21:50:58] 
INFO [2025-10-15 21:50:58] $filename
INFO [2025-10-15 21:50:58] NULL
INFO [2025-10-15 21:50:58] 
INFO [2025-10-15 21:50:58] $scaled
INFO [2025-10-15 21:50:58] [1] FALSE
INFO [2025-10-15 21:50:58] 
INFO [2025-10-15 21:50:58] $euler.d
INFO [2025-10-15 21:50:58] [1] FALSE
INFO [2025-10-15 21:50:58] 
INFO [2025-10-15 21:50:58] $cat.cex
INFO [2025-10-15 21:50:58] [1] 1
INFO [2025-10-15 21:50:58] 
INFO [2025-10-15 21:50:58] $cat.col
INFO [2025-10-15 21:50:58] [1] "black"
INFO [2025-10-15 21:50:58] 
INFO [2025-10-15 21:50:58] $cat.fontface
INFO [2025-10-15 21:50:58] [1] "plain"
INFO [2025-10-15 21:50:58] 
INFO [2025-10-15 21:50:58] $cat.fontfamily
INFO [2025-10-15 21:50:58] [1] "serif"
INFO [2025-10-15 21:50:58] 
INFO [2025-10-15 21:50:58] $x
INFO [2025-10-15 21:50:58] $x$TF1
INFO [2025-10-15 21:50:58] [1] 1 2 3
INFO [2025-10-15 21:50:58] 
INFO [2025-10-15 21:50:58] $x$TF2
INFO [2025-10-15 21:50:58] [1] 1 2 3
INFO [2025-10-15 21:50:58] 
INFO [2025-10-15 21:50:58] 
INFO [2025-10-15 21:50:58] $disable.logging
INFO [2025-10-15 21:50:58] [1] TRUE
INFO [2025-10-15 21:50:58] 
INFO [2025-10-15 21:50:58] $filename
INFO [2025-10-15 21:50:58] NULL
INFO [2025-10-15 21:50:58] 
INFO [2025-10-15 21:50:58] $scaled
INFO [2025-10-15 21:50:58] [1] FALSE
INFO [2025-10-15 21:50:58] 
INFO [2025-10-15 21:50:58] $euler.d
INFO [2025-10-15 21:50:58] [1] FALSE
INFO [2025-10-15 21:50:58] 
INFO [2025-10-15 21:50:58] $cat.cex
INFO [2025-10-15 21:50:58] [1] 1
INFO [2025-10-15 21:50:58] 
INFO [2025-10-15 21:50:58] $cat.col
INFO [2025-10-15 21:50:58] [1] "black"
INFO [2025-10-15 21:50:58] 
INFO [2025-10-15 21:50:58] $cat.fontface
INFO [2025-10-15 21:50:58] [1] "plain"
INFO [2025-10-15 21:50:58] 
INFO [2025-10-15 21:50:58] $cat.fontfamily
INFO [2025-10-15 21:50:58] [1] "serif"
INFO [2025-10-15 21:50:58] 
INFO [2025-10-15 21:50:58] $x
INFO [2025-10-15 21:50:58] $x$TF1
INFO [2025-10-15 21:50:58] [1] 4 5 6
INFO [2025-10-15 21:50:58] 
INFO [2025-10-15 21:50:58] $x$TF2
INFO [2025-10-15 21:50:58] [1] 1 2 3
INFO [2025-10-15 21:50:58] 
INFO [2025-10-15 21:50:58] 
INFO [2025-10-15 21:50:58] $disable.logging
INFO [2025-10-15 21:50:58] [1] TRUE
INFO [2025-10-15 21:50:58] 
INFO [2025-10-15 21:50:58] $filename
INFO [2025-10-15 21:50:58] NULL
INFO [2025-10-15 21:50:58] 
INFO [2025-10-15 21:50:59] $scaled
INFO [2025-10-15 21:50:59] [1] FALSE
INFO [2025-10-15 21:50:59] 
INFO [2025-10-15 21:50:59] $euler.d
INFO [2025-10-15 21:50:59] [1] FALSE
INFO [2025-10-15 21:50:59] 
INFO [2025-10-15 21:50:59] $cat.cex
INFO [2025-10-15 21:50:59] [1] 1
INFO [2025-10-15 21:50:59] 
INFO [2025-10-15 21:50:59] $cat.col
INFO [2025-10-15 21:50:59] [1] "black"
INFO [2025-10-15 21:50:59] 
INFO [2025-10-15 21:50:59] $cat.fontface
INFO [2025-10-15 21:50:59] [1] "plain"
INFO [2025-10-15 21:50:59] 
INFO [2025-10-15 21:50:59] $cat.fontfamily
INFO [2025-10-15 21:50:59] [1] "serif"
INFO [2025-10-15 21:50:59] 
INFO [2025-10-15 21:50:59] $x
INFO [2025-10-15 21:50:59] $x$TF1
INFO [2025-10-15 21:50:59] [1] 4 5 6
INFO [2025-10-15 21:50:59] 
INFO [2025-10-15 21:50:59] $x$TF2
INFO [2025-10-15 21:50:59] [1] 1 2 3
INFO [2025-10-15 21:50:59] 
INFO [2025-10-15 21:50:59] 
INFO [2025-10-15 21:50:59] $disable.logging
INFO [2025-10-15 21:50:59] [1] TRUE
INFO [2025-10-15 21:50:59] 
INFO [2025-10-15 21:50:59] $filename
INFO [2025-10-15 21:50:59] NULL
INFO [2025-10-15 21:50:59] 
INFO [2025-10-15 21:50:59] $scaled
INFO [2025-10-15 21:50:59] [1] FALSE
INFO [2025-10-15 21:50:59] 
INFO [2025-10-15 21:50:59] $euler.d
INFO [2025-10-15 21:50:59] [1] FALSE
INFO [2025-10-15 21:50:59] 
INFO [2025-10-15 21:50:59] $cat.cex
INFO [2025-10-15 21:50:59] [1] 1
INFO [2025-10-15 21:50:59] 
INFO [2025-10-15 21:50:59] $cat.col
INFO [2025-10-15 21:50:59] [1] "black"
INFO [2025-10-15 21:50:59] 
INFO [2025-10-15 21:50:59] $cat.fontface
INFO [2025-10-15 21:50:59] [1] "plain"
INFO [2025-10-15 21:50:59] 
INFO [2025-10-15 21:50:59] $cat.fontfamily
INFO [2025-10-15 21:50:59] [1] "serif"
INFO [2025-10-15 21:50:59] 
INFO [2025-10-15 21:50:59] $x
INFO [2025-10-15 21:50:59] $x$TF1
INFO [2025-10-15 21:50:59] [1] 4 5 6
INFO [2025-10-15 21:50:59] 
INFO [2025-10-15 21:50:59] $x$TF2
INFO [2025-10-15 21:50:59] [1] 1 2 3
INFO [2025-10-15 21:50:59] 
INFO [2025-10-15 21:50:59] $x$TF3
INFO [2025-10-15 21:50:59] [1] 2 3 6
INFO [2025-10-15 21:50:59] 
INFO [2025-10-15 21:50:59] 
INFO [2025-10-15 21:50:59] $disable.logging
INFO [2025-10-15 21:50:59] [1] TRUE
INFO [2025-10-15 21:50:59] 
INFO [2025-10-15 21:50:59] $filename
INFO [2025-10-15 21:50:59] NULL
INFO [2025-10-15 21:50:59] 
INFO [2025-10-15 21:50:59] $scaled
INFO [2025-10-15 21:50:59] [1] FALSE
INFO [2025-10-15 21:50:59] 
INFO [2025-10-15 21:50:59] $euler.d
INFO [2025-10-15 21:50:59] [1] FALSE
INFO [2025-10-15 21:50:59] 
INFO [2025-10-15 21:50:59] $cat.cex
INFO [2025-10-15 21:50:59] [1] 1
INFO [2025-10-15 21:50:59] 
INFO [2025-10-15 21:50:59] $cat.col
INFO [2025-10-15 21:50:59] [1] "black"
INFO [2025-10-15 21:50:59] 
INFO [2025-10-15 21:50:59] $cat.fontface
INFO [2025-10-15 21:50:59] [1] "plain"
INFO [2025-10-15 21:50:59] 
INFO [2025-10-15 21:50:59] $cat.fontfamily
INFO [2025-10-15 21:50:59] [1] "serif"
INFO [2025-10-15 21:50:59] 
INFO [2025-10-15 21:50:59] $x
INFO [2025-10-15 21:50:59] $x$TF1
INFO [2025-10-15 21:50:59] [1] 3 4 5
INFO [2025-10-15 21:50:59] 
INFO [2025-10-15 21:50:59] $x$TF2
INFO [2025-10-15 21:50:59] [1] 1 2 5
INFO [2025-10-15 21:50:59] 
INFO [2025-10-15 21:50:59] $x$TF3
INFO [2025-10-15 21:50:59] [1] 1 2 5
INFO [2025-10-15 21:50:59] 
INFO [2025-10-15 21:50:59] 
INFO [2025-10-15 21:50:59] $disable.logging
INFO [2025-10-15 21:50:59] [1] TRUE
INFO [2025-10-15 21:50:59] 
INFO [2025-10-15 21:50:59] $filename
INFO [2025-10-15 21:50:59] NULL
INFO [2025-10-15 21:50:59] 
INFO [2025-10-15 21:51:00] $scaled
INFO [2025-10-15 21:51:00] [1] FALSE
INFO [2025-10-15 21:51:00] 
INFO [2025-10-15 21:51:00] $euler.d
INFO [2025-10-15 21:51:00] [1] FALSE
INFO [2025-10-15 21:51:00] 
INFO [2025-10-15 21:51:00] $cat.cex
INFO [2025-10-15 21:51:00] [1] 1
INFO [2025-10-15 21:51:00] 
INFO [2025-10-15 21:51:00] $cat.col
INFO [2025-10-15 21:51:00] [1] "black"
INFO [2025-10-15 21:51:00] 
INFO [2025-10-15 21:51:00] $cat.fontface
INFO [2025-10-15 21:51:00] [1] "plain"
INFO [2025-10-15 21:51:00] 
INFO [2025-10-15 21:51:00] $cat.fontfamily
INFO [2025-10-15 21:51:00] [1] "serif"
INFO [2025-10-15 21:51:00] 
INFO [2025-10-15 21:51:00] $x
INFO [2025-10-15 21:51:00] $x$TF1
INFO [2025-10-15 21:51:00] [1] 3 4 5
INFO [2025-10-15 21:51:00] 
INFO [2025-10-15 21:51:00] $x$TF2
INFO [2025-10-15 21:51:00] [1] 1 2 5
INFO [2025-10-15 21:51:00] 
INFO [2025-10-15 21:51:00] $x$TF3
INFO [2025-10-15 21:51:00] [1] 1 2 5
INFO [2025-10-15 21:51:00] 
INFO [2025-10-15 21:51:00] $x$TF4
INFO [2025-10-15 21:51:00] [1] 1 2 5
INFO [2025-10-15 21:51:00] 
INFO [2025-10-15 21:51:00] 
INFO [2025-10-15 21:51:00] $disable.logging
INFO [2025-10-15 21:51:00] [1] TRUE
INFO [2025-10-15 21:51:00] 
INFO [2025-10-15 21:51:00] $filename
INFO [2025-10-15 21:51:00] NULL
INFO [2025-10-15 21:51:00] 
[ FAIL 0 | WARN 3 | SKIP 6 | PASS 320 ]

══ Skipped tests (6) ═══════════════════════════════════════════════════════════
• empty test (6): 'test_binOverGene.R:1:1', 'test_binOverRegions.R:1:1',
  'test_enrichmentPlot.R:1:1', 'test_getAnnotation.R:1:1',
  'test_reCenterPeaks.R:1:1', 'test_write2FASTA.R:1:1'

[ FAIL 0 | WARN 3 | SKIP 6 | PASS 320 ]
> 
> proc.time()
   user  system elapsed 
165.416   5.482 172.638 

Example timings

ChIPpeakAnno.Rcheck/ChIPpeakAnno-Ex.timings

nameusersystemelapsed
ChIPpeakAnno-package000
ExonPlusUtr.human.GRCh373.6240.1883.814
HOT.spots0.1350.0150.148
IDRfilter0.0000.0010.000
Peaks.Ste12.Replicate10.0470.0010.047
Peaks.Ste12.Replicate20.0100.0010.012
Peaks.Ste12.Replicate30.0100.0000.011
TSS.human.GRCh370.1100.0060.114
TSS.human.GRCh380.2210.0070.229
TSS.human.NCBI360.1030.0070.110
TSS.mouse.GRCm380.0980.0170.116
TSS.mouse.NCBIM370.0870.0070.096
TSS.rat.RGSC3.40.0770.0040.081
TSS.rat.Rnor_5.00.0660.0050.070
TSS.zebrafish.Zv80.0690.0060.076
TSS.zebrafish.Zv90.0840.0100.092
addAncestors0.9160.0600.977
addGeneIDs0.7210.0460.767
addMetadata1.2260.0821.309
annoGR0.0010.0000.000
annoPeaks2.6930.4623.677
annotatePeakInBatch11.855 1.09012.950
annotatedPeak0.0580.0030.061
assignChromosomeRegion0.0000.0010.001
bdp000
binOverFeature0.7530.0450.799
binOverGene0.0010.0000.001
binOverRegions0.0010.0000.000
condenseMatrixByColnames0.0090.0020.010
convert2EntrezID0.3500.0070.358
countPatternInSeqs0.1900.0140.204
cumulativePercentage0.0000.0010.000
downstreams0.0220.0050.027
egOrgMap0.0010.0000.001
enrichedGO0.0020.0010.003
enrichmentPlot0.6520.0490.702
estFragmentLength000
estLibSize0.0000.0010.000
featureAlignedDistribution0.2230.0160.239
featureAlignedExtendSignal0.0010.0010.002
featureAlignedHeatmap0.3690.0300.399
featureAlignedSignal0.1760.0530.229
findEnhancers22.947 0.83923.793
findMotifsInPromoterSeqs13.939 0.52514.465
findOverlappingPeaks0.0010.0000.002
findOverlapsOfPeaks1.7440.0431.788
genomicElementDistribution0.0000.0010.001
genomicElementUpSetR0.0010.0000.000
getAllPeakSequence0.5880.0220.610
getAnnotation0.0010.0000.001
getEnrichedGO0.0760.0030.079
getEnrichedPATH0.0000.0010.001
getGO000
getGeneSeq0.0010.0000.002
getUniqueGOidCount0.0000.0010.001
getVennCounts0.0000.0010.001
hyperGtest0.0010.0000.002
makeVennDiagram0.0010.0020.003
mergePlusMinusPeaks0.0000.0000.001
metagenePlot2.1440.0562.203
myPeakList0.0180.0000.019
oligoFrequency0.1140.0050.118
oligoSummary0.0000.0010.001
peakPermTest0.0020.0000.002
peaks10.0070.0000.008
peaks20.0070.0000.007
peaks30.0070.0010.007
peaksNearBDP0.0000.0010.000
pie10.0040.0020.005
plotBinOverRegions0.0010.0000.000
preparePool0.0000.0010.001
reCenterPeaks0.0250.0000.024
summarizeOverlapsByBins5.7920.5516.058
summarizePatternInPeaks1.2760.1731.451
tileCount0.1890.2130.367
tileGRanges0.1490.1200.038
toGRanges0.0760.0080.084
translatePattern0.0000.0000.001
wgEncodeTfbsV30.2180.0190.236
write2FASTA0.0150.0010.016
xget0.0930.0120.105