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This page was generated on 2025-08-30 12:04 -0400 (Sat, 30 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4615
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4562
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4541
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 342/2320HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPpeakAnno 3.43.1  (landing page)
Jianhong Ou
Snapshot Date: 2025-08-29 13:45 -0400 (Fri, 29 Aug 2025)
git_url: https://git.bioconductor.org/packages/ChIPpeakAnno
git_branch: devel
git_last_commit: b1cad5f
git_last_commit_date: 2025-07-11 09:55:39 -0400 (Fri, 11 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for ChIPpeakAnno on nebbiolo2

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: 3.43.1
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ChIPpeakAnno_3.43.1.tar.gz
StartedAt: 2025-08-29 21:11:06 -0400 (Fri, 29 Aug 2025)
EndedAt: 2025-08-29 21:35:47 -0400 (Fri, 29 Aug 2025)
EllapsedTime: 1480.6 seconds
RetCode: 0
Status:   OK  
CheckDir: ChIPpeakAnno.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ChIPpeakAnno_3.43.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-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 ‘3.43.1’
* 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 21.1Mb
  sub-directories of 1Mb or more:
    R         1.0Mb
    data     12.6Mb
    extdata   7.2Mb
* 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            23.344  0.330  23.674
findMotifsInPromoterSeqs 14.000  0.217  14.223
annotatePeakInBatch      12.189  0.321  12.512
summarizeOverlapsByBins   5.391  0.478   5.614
* 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-3.22-bioc/R/bin/R CMD INSTALL ChIPpeakAnno
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘ChIPpeakAnno’ ...
** this is package ‘ChIPpeakAnno’ version ‘3.43.1’
** 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: Seqinfo
[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 [2025-08-29 21:20:58] $cat.cex
INFO [2025-08-29 21:20:58] [1] 1
INFO [2025-08-29 21:20:58] 
INFO [2025-08-29 21:20:58] $cat.col
INFO [2025-08-29 21:20:58] [1] "black"
INFO [2025-08-29 21:20:58] 
INFO [2025-08-29 21:20:58] $cat.fontface
INFO [2025-08-29 21:20:58] [1] "plain"
INFO [2025-08-29 21:20:58] 
INFO [2025-08-29 21:20:58] $cat.fontfamily
INFO [2025-08-29 21:20:58] [1] "serif"
INFO [2025-08-29 21:20:58] 
INFO [2025-08-29 21:20:58] $x
INFO [2025-08-29 21:20:58] $x$TF1
INFO [2025-08-29 21:20:58] [1] 3 4 5
INFO [2025-08-29 21:20:58] 
INFO [2025-08-29 21:20:58] $x$TF2
INFO [2025-08-29 21:20:58] [1] 1 2 3 4 5
INFO [2025-08-29 21:20:58] 
INFO [2025-08-29 21:20:58] 
INFO [2025-08-29 21:20:58] $disable.logging
INFO [2025-08-29 21:20:58] [1] TRUE
INFO [2025-08-29 21:20:58] 
INFO [2025-08-29 21:20:58] $filename
INFO [2025-08-29 21:20:58] NULL
INFO [2025-08-29 21:20:58] 
INFO [2025-08-29 21:20:58] $cat.cex
INFO [2025-08-29 21:20:58] [1] 1
INFO [2025-08-29 21:20:58] 
INFO [2025-08-29 21:20:58] $cat.col
INFO [2025-08-29 21:20:58] [1] "black"
INFO [2025-08-29 21:20:58] 
INFO [2025-08-29 21:20:58] $cat.fontface
INFO [2025-08-29 21:20:58] [1] "plain"
INFO [2025-08-29 21:20:58] 
INFO [2025-08-29 21:20:58] $cat.fontfamily
INFO [2025-08-29 21:20:58] [1] "serif"
INFO [2025-08-29 21:20:58] 
INFO [2025-08-29 21:20:58] $x
INFO [2025-08-29 21:20:58] $x$TF1
INFO [2025-08-29 21:20:58] [1] 3 4 5
INFO [2025-08-29 21:20:58] 
INFO [2025-08-29 21:20:58] $x$TF2
INFO [2025-08-29 21:20:58] [1] 1 2 4 5
INFO [2025-08-29 21:20:58] 
INFO [2025-08-29 21:20:58] $x$TF3
INFO [2025-08-29 21:20:58] [1] 3 4 5
INFO [2025-08-29 21:20:58] 
INFO [2025-08-29 21:20:58] $x$TF4
INFO [2025-08-29 21:20:58] [1] 1 2 4 5
INFO [2025-08-29 21:20:58] 
INFO [2025-08-29 21:20:58] 
INFO [2025-08-29 21:20:58] $disable.logging
INFO [2025-08-29 21:20:58] [1] TRUE
INFO [2025-08-29 21:20:58] 
INFO [2025-08-29 21:20:58] $filename
INFO [2025-08-29 21:20:58] NULL
INFO [2025-08-29 21:20:58] 
INFO [2025-08-29 21:20:59] $scaled
INFO [2025-08-29 21:20:59] [1] FALSE
INFO [2025-08-29 21:20:59] 
INFO [2025-08-29 21:20:59] $euler.d
INFO [2025-08-29 21:20:59] [1] FALSE
INFO [2025-08-29 21:20:59] 
INFO [2025-08-29 21:20:59] $cat.cex
INFO [2025-08-29 21:20:59] [1] 1
INFO [2025-08-29 21:20:59] 
INFO [2025-08-29 21:20:59] $cat.col
INFO [2025-08-29 21:20:59] [1] "black"
INFO [2025-08-29 21:20:59] 
INFO [2025-08-29 21:20:59] $cat.fontface
INFO [2025-08-29 21:20:59] [1] "plain"
INFO [2025-08-29 21:20:59] 
INFO [2025-08-29 21:20:59] $cat.fontfamily
INFO [2025-08-29 21:20:59] [1] "serif"
INFO [2025-08-29 21:20:59] 
INFO [2025-08-29 21:20:59] $x
INFO [2025-08-29 21:20:59] $x$TF1
INFO [2025-08-29 21:20:59] [1] 1 2 3
INFO [2025-08-29 21:20:59] 
INFO [2025-08-29 21:20:59] $x$TF2
INFO [2025-08-29 21:20:59] [1] 1 2 3
INFO [2025-08-29 21:20:59] 
INFO [2025-08-29 21:20:59] 
INFO [2025-08-29 21:20:59] $disable.logging
INFO [2025-08-29 21:20:59] [1] TRUE
INFO [2025-08-29 21:20:59] 
INFO [2025-08-29 21:20:59] $filename
INFO [2025-08-29 21:20:59] NULL
INFO [2025-08-29 21:20:59] 
INFO [2025-08-29 21:20:59] $scaled
INFO [2025-08-29 21:20:59] [1] FALSE
INFO [2025-08-29 21:20:59] 
INFO [2025-08-29 21:20:59] $euler.d
INFO [2025-08-29 21:20:59] [1] FALSE
INFO [2025-08-29 21:20:59] 
INFO [2025-08-29 21:20:59] $cat.cex
INFO [2025-08-29 21:20:59] [1] 1
INFO [2025-08-29 21:20:59] 
INFO [2025-08-29 21:20:59] $cat.col
INFO [2025-08-29 21:20:59] [1] "black"
INFO [2025-08-29 21:20:59] 
INFO [2025-08-29 21:20:59] $cat.fontface
INFO [2025-08-29 21:20:59] [1] "plain"
INFO [2025-08-29 21:20:59] 
INFO [2025-08-29 21:20:59] $cat.fontfamily
INFO [2025-08-29 21:20:59] [1] "serif"
INFO [2025-08-29 21:20:59] 
INFO [2025-08-29 21:20:59] $x
INFO [2025-08-29 21:20:59] $x$TF1
INFO [2025-08-29 21:20:59] [1] 4 5 6
INFO [2025-08-29 21:20:59] 
INFO [2025-08-29 21:20:59] $x$TF2
INFO [2025-08-29 21:20:59] [1] 1 2 3
INFO [2025-08-29 21:20:59] 
INFO [2025-08-29 21:20:59] 
INFO [2025-08-29 21:20:59] $disable.logging
INFO [2025-08-29 21:20:59] [1] TRUE
INFO [2025-08-29 21:20:59] 
INFO [2025-08-29 21:20:59] $filename
INFO [2025-08-29 21:20:59] NULL
INFO [2025-08-29 21:20:59] 
INFO [2025-08-29 21:20:59] $scaled
INFO [2025-08-29 21:20:59] [1] FALSE
INFO [2025-08-29 21:20:59] 
INFO [2025-08-29 21:20:59] $euler.d
INFO [2025-08-29 21:20:59] [1] FALSE
INFO [2025-08-29 21:20:59] 
INFO [2025-08-29 21:20:59] $cat.cex
INFO [2025-08-29 21:20:59] [1] 1
INFO [2025-08-29 21:20:59] 
INFO [2025-08-29 21:20:59] $cat.col
INFO [2025-08-29 21:20:59] [1] "black"
INFO [2025-08-29 21:20:59] 
INFO [2025-08-29 21:20:59] $cat.fontface
INFO [2025-08-29 21:20:59] [1] "plain"
INFO [2025-08-29 21:20:59] 
INFO [2025-08-29 21:20:59] $cat.fontfamily
INFO [2025-08-29 21:20:59] [1] "serif"
INFO [2025-08-29 21:20:59] 
INFO [2025-08-29 21:20:59] $x
INFO [2025-08-29 21:20:59] $x$TF1
INFO [2025-08-29 21:20:59] [1] 4 5 6
INFO [2025-08-29 21:20:59] 
INFO [2025-08-29 21:20:59] $x$TF2
INFO [2025-08-29 21:20:59] [1] 1 2 3
INFO [2025-08-29 21:20:59] 
INFO [2025-08-29 21:20:59] 
INFO [2025-08-29 21:20:59] $disable.logging
INFO [2025-08-29 21:20:59] [1] TRUE
INFO [2025-08-29 21:20:59] 
INFO [2025-08-29 21:20:59] $filename
INFO [2025-08-29 21:20:59] NULL
INFO [2025-08-29 21:20:59] 
INFO [2025-08-29 21:20:59] $scaled
INFO [2025-08-29 21:20:59] [1] FALSE
INFO [2025-08-29 21:20:59] 
INFO [2025-08-29 21:20:59] $euler.d
INFO [2025-08-29 21:20:59] [1] FALSE
INFO [2025-08-29 21:20:59] 
INFO [2025-08-29 21:20:59] $cat.cex
INFO [2025-08-29 21:20:59] [1] 1
INFO [2025-08-29 21:20:59] 
INFO [2025-08-29 21:20:59] $cat.col
INFO [2025-08-29 21:20:59] [1] "black"
INFO [2025-08-29 21:20:59] 
INFO [2025-08-29 21:20:59] $cat.fontface
INFO [2025-08-29 21:20:59] [1] "plain"
INFO [2025-08-29 21:20:59] 
INFO [2025-08-29 21:20:59] $cat.fontfamily
INFO [2025-08-29 21:20:59] [1] "serif"
INFO [2025-08-29 21:20:59] 
INFO [2025-08-29 21:20:59] $x
INFO [2025-08-29 21:20:59] $x$TF1
INFO [2025-08-29 21:20:59] [1] 4 5 6
INFO [2025-08-29 21:20:59] 
INFO [2025-08-29 21:20:59] $x$TF2
INFO [2025-08-29 21:20:59] [1] 1 2 3
INFO [2025-08-29 21:20:59] 
INFO [2025-08-29 21:20:59] $x$TF3
INFO [2025-08-29 21:20:59] [1] 2 3 6
INFO [2025-08-29 21:20:59] 
INFO [2025-08-29 21:20:59] 
INFO [2025-08-29 21:20:59] $disable.logging
INFO [2025-08-29 21:20:59] [1] TRUE
INFO [2025-08-29 21:20:59] 
INFO [2025-08-29 21:20:59] $filename
INFO [2025-08-29 21:20:59] NULL
INFO [2025-08-29 21:20:59] 
INFO [2025-08-29 21:21:00] $scaled
INFO [2025-08-29 21:21:00] [1] FALSE
INFO [2025-08-29 21:21:00] 
INFO [2025-08-29 21:21:00] $euler.d
INFO [2025-08-29 21:21:00] [1] FALSE
INFO [2025-08-29 21:21:00] 
INFO [2025-08-29 21:21:00] $cat.cex
INFO [2025-08-29 21:21:00] [1] 1
INFO [2025-08-29 21:21:00] 
INFO [2025-08-29 21:21:00] $cat.col
INFO [2025-08-29 21:21:00] [1] "black"
INFO [2025-08-29 21:21:00] 
INFO [2025-08-29 21:21:00] $cat.fontface
INFO [2025-08-29 21:21:00] [1] "plain"
INFO [2025-08-29 21:21:00] 
INFO [2025-08-29 21:21:00] $cat.fontfamily
INFO [2025-08-29 21:21:00] [1] "serif"
INFO [2025-08-29 21:21:00] 
INFO [2025-08-29 21:21:00] $x
INFO [2025-08-29 21:21:00] $x$TF1
INFO [2025-08-29 21:21:00] [1] 3 4 5
INFO [2025-08-29 21:21:00] 
INFO [2025-08-29 21:21:00] $x$TF2
INFO [2025-08-29 21:21:00] [1] 1 2 5
INFO [2025-08-29 21:21:00] 
INFO [2025-08-29 21:21:00] $x$TF3
INFO [2025-08-29 21:21:00] [1] 1 2 5
INFO [2025-08-29 21:21:00] 
INFO [2025-08-29 21:21:00] 
INFO [2025-08-29 21:21:00] $disable.logging
INFO [2025-08-29 21:21:00] [1] TRUE
INFO [2025-08-29 21:21:00] 
INFO [2025-08-29 21:21:00] $filename
INFO [2025-08-29 21:21:00] NULL
INFO [2025-08-29 21:21:00] 
INFO [2025-08-29 21:21:00] $scaled
INFO [2025-08-29 21:21:00] [1] FALSE
INFO [2025-08-29 21:21:00] 
INFO [2025-08-29 21:21:00] $euler.d
INFO [2025-08-29 21:21:00] [1] FALSE
INFO [2025-08-29 21:21:00] 
INFO [2025-08-29 21:21:00] $cat.cex
INFO [2025-08-29 21:21:00] [1] 1
INFO [2025-08-29 21:21:00] 
INFO [2025-08-29 21:21:00] $cat.col
INFO [2025-08-29 21:21:00] [1] "black"
INFO [2025-08-29 21:21:00] 
INFO [2025-08-29 21:21:00] $cat.fontface
INFO [2025-08-29 21:21:00] [1] "plain"
INFO [2025-08-29 21:21:00] 
INFO [2025-08-29 21:21:00] $cat.fontfamily
INFO [2025-08-29 21:21:00] [1] "serif"
INFO [2025-08-29 21:21:00] 
INFO [2025-08-29 21:21:00] $x
INFO [2025-08-29 21:21:00] $x$TF1
INFO [2025-08-29 21:21:00] [1] 3 4 5
INFO [2025-08-29 21:21:00] 
INFO [2025-08-29 21:21:00] $x$TF2
INFO [2025-08-29 21:21:00] [1] 1 2 5
INFO [2025-08-29 21:21:00] 
INFO [2025-08-29 21:21:00] $x$TF3
INFO [2025-08-29 21:21:00] [1] 1 2 5
INFO [2025-08-29 21:21:00] 
INFO [2025-08-29 21:21:00] $x$TF4
INFO [2025-08-29 21:21:00] [1] 1 2 5
INFO [2025-08-29 21:21:00] 
INFO [2025-08-29 21:21:00] 
INFO [2025-08-29 21:21:00] $disable.logging
INFO [2025-08-29 21:21:00] [1] TRUE
INFO [2025-08-29 21:21:00] 
INFO [2025-08-29 21:21:00] $filename
INFO [2025-08-29 21:21:00] NULL
INFO [2025-08-29 21:21:00] 
[ FAIL 0 | WARN 2 | SKIP 6 | PASS 324 ]

══ 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 2 | SKIP 6 | PASS 324 ]
> 
> proc.time()
   user  system elapsed 
172.164   3.379 176.368 

Example timings

ChIPpeakAnno.Rcheck/ChIPpeakAnno-Ex.timings

nameusersystemelapsed
ChIPpeakAnno-package0.0010.0000.000
ExonPlusUtr.human.GRCh373.7380.1823.920
HOT.spots0.1340.0130.147
IDRfilter0.0010.0000.000
Peaks.Ste12.Replicate10.0510.0010.053
Peaks.Ste12.Replicate20.0120.0000.012
Peaks.Ste12.Replicate30.0110.0000.011
TSS.human.GRCh370.1750.0110.185
TSS.human.GRCh380.1520.0000.152
TSS.human.NCBI360.1080.0060.114
TSS.mouse.GRCm380.1050.0040.109
TSS.mouse.NCBIM370.0900.0050.095
TSS.rat.RGSC3.40.0750.0060.081
TSS.rat.Rnor_5.00.0640.0050.069
TSS.zebrafish.Zv80.0710.0030.074
TSS.zebrafish.Zv90.0820.0090.092
addAncestors0.9080.0350.943
addGeneIDs0.8320.0210.853
addMetadata1.0010.1021.104
annoGR0.0000.0000.001
annoPeaks2.8060.1702.977
annotatePeakInBatch12.189 0.32112.512
annotatedPeak0.060.000.06
assignChromosomeRegion0.0010.0000.000
bdp000
binOverFeature0.7860.0110.797
binOverGene000
binOverRegions0.0010.0000.000
condenseMatrixByColnames0.0090.0010.010
convert2EntrezID0.3660.0030.369
countPatternInSeqs0.1700.0010.172
cumulativePercentage000
downstreams0.0230.0000.023
egOrgMap0.0010.0000.001
enrichedGO0.0020.0000.002
enrichmentPlot0.4570.0010.458
estFragmentLength0.0010.0000.000
estLibSize0.0000.0000.001
featureAlignedDistribution0.2160.0010.217
featureAlignedExtendSignal0.0010.0000.001
featureAlignedHeatmap0.3950.0010.397
featureAlignedSignal0.1820.0060.187
findEnhancers23.344 0.33023.674
findMotifsInPromoterSeqs14.000 0.21714.223
findOverlappingPeaks0.0000.0010.001
findOverlapsOfPeaks1.6320.0151.648
genomicElementDistribution0.0010.0000.001
genomicElementUpSetR000
getAllPeakSequence0.4870.0170.505
getAnnotation0.0000.0000.001
getEnrichedGO0.0060.0020.008
getEnrichedPATH0.0010.0000.000
getGO000
getGeneSeq0.0000.0000.001
getUniqueGOidCount0.0000.0000.001
getVennCounts0.0010.0000.001
hyperGtest0.0010.0000.001
makeVennDiagram0.0020.0000.001
mergePlusMinusPeaks0.0010.0000.000
metagenePlot1.8350.0501.885
myPeakList0.0130.0010.015
oligoFrequency0.0880.0020.090
oligoSummary0.0000.0010.001
peakPermTest0.0010.0000.001
peaks10.0060.0000.007
peaks20.0050.0010.007
peaks30.0050.0010.006
peaksNearBDP000
pie10.0050.0000.004
plotBinOverRegions0.0010.0000.001
preparePool0.0000.0000.001
reCenterPeaks0.0210.0010.022
summarizeOverlapsByBins5.3910.4785.614
summarizePatternInPeaks1.1980.1561.355
tileCount0.1890.1930.328
tileGRanges0.1320.1090.038
toGRanges0.0810.0090.090
translatePattern000
wgEncodeTfbsV30.2240.0070.231
write2FASTA0.0150.0010.016
xget0.0960.0080.104