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This page was generated on 2025-08-23 12:04 -0400 (Sat, 23 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4821
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4599
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4553
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4539
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 342/2319HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPpeakAnno 3.43.1  (landing page)
Jianhong Ou
Snapshot Date: 2025-08-22 13:45 -0400 (Fri, 22 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 lconway

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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ChIPpeakAnno_3.43.1.tar.gz
StartedAt: 2025-08-22 19:43:18 -0400 (Fri, 22 Aug 2025)
EndedAt: 2025-08-22 19:55:10 -0400 (Fri, 22 Aug 2025)
EllapsedTime: 711.2 seconds
RetCode: 0
Status:   OK  
CheckDir: ChIPpeakAnno.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ChIPpeakAnno_3.43.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/ChIPpeakAnno.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 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            27.882  0.929  28.982
findMotifsInPromoterSeqs 17.545  0.459  18.303
annotatePeakInBatch      14.137  0.806  15.049
summarizeOverlapsByBins   5.614  0.486   5.802
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

ChIPpeakAnno.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ChIPpeakAnno
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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-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.

> 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 [2025-08-22 19:54:41] $cat.cex
INFO [2025-08-22 19:54:41] [1] 1
INFO [2025-08-22 19:54:41] 
INFO [2025-08-22 19:54:41] $cat.col
INFO [2025-08-22 19:54:41] [1] "black"
INFO [2025-08-22 19:54:41] 
INFO [2025-08-22 19:54:41] $cat.fontface
INFO [2025-08-22 19:54:41] [1] "plain"
INFO [2025-08-22 19:54:41] 
INFO [2025-08-22 19:54:41] $cat.fontfamily
INFO [2025-08-22 19:54:41] [1] "serif"
INFO [2025-08-22 19:54:41] 
INFO [2025-08-22 19:54:41] $x
INFO [2025-08-22 19:54:41] $x$TF1
INFO [2025-08-22 19:54:41] [1] 3 4 5
INFO [2025-08-22 19:54:41] 
INFO [2025-08-22 19:54:41] $x$TF2
INFO [2025-08-22 19:54:41] [1] 1 2 3 4 5
INFO [2025-08-22 19:54:41] 
INFO [2025-08-22 19:54:41] 
INFO [2025-08-22 19:54:41] $disable.logging
INFO [2025-08-22 19:54:41] [1] TRUE
INFO [2025-08-22 19:54:41] 
INFO [2025-08-22 19:54:41] $filename
INFO [2025-08-22 19:54:41] NULL
INFO [2025-08-22 19:54:41] 
INFO [2025-08-22 19:54:41] $cat.cex
INFO [2025-08-22 19:54:41] [1] 1
INFO [2025-08-22 19:54:41] 
INFO [2025-08-22 19:54:41] $cat.col
INFO [2025-08-22 19:54:41] [1] "black"
INFO [2025-08-22 19:54:41] 
INFO [2025-08-22 19:54:41] $cat.fontface
INFO [2025-08-22 19:54:41] [1] "plain"
INFO [2025-08-22 19:54:41] 
INFO [2025-08-22 19:54:41] $cat.fontfamily
INFO [2025-08-22 19:54:41] [1] "serif"
INFO [2025-08-22 19:54:41] 
INFO [2025-08-22 19:54:41] $x
INFO [2025-08-22 19:54:41] $x$TF1
INFO [2025-08-22 19:54:41] [1] 3 4 5
INFO [2025-08-22 19:54:41] 
INFO [2025-08-22 19:54:41] $x$TF2
INFO [2025-08-22 19:54:41] [1] 1 2 4 5
INFO [2025-08-22 19:54:41] 
INFO [2025-08-22 19:54:41] $x$TF3
INFO [2025-08-22 19:54:41] [1] 3 4 5
INFO [2025-08-22 19:54:41] 
INFO [2025-08-22 19:54:41] $x$TF4
INFO [2025-08-22 19:54:41] [1] 1 2 4 5
INFO [2025-08-22 19:54:41] 
INFO [2025-08-22 19:54:41] 
INFO [2025-08-22 19:54:41] $disable.logging
INFO [2025-08-22 19:54:41] [1] TRUE
INFO [2025-08-22 19:54:41] 
INFO [2025-08-22 19:54:41] $filename
INFO [2025-08-22 19:54:41] NULL
INFO [2025-08-22 19:54:41] 
INFO [2025-08-22 19:54:42] $scaled
INFO [2025-08-22 19:54:42] [1] FALSE
INFO [2025-08-22 19:54:42] 
INFO [2025-08-22 19:54:42] $euler.d
INFO [2025-08-22 19:54:42] [1] FALSE
INFO [2025-08-22 19:54:42] 
INFO [2025-08-22 19:54:42] $cat.cex
INFO [2025-08-22 19:54:42] [1] 1
INFO [2025-08-22 19:54:42] 
INFO [2025-08-22 19:54:42] $cat.col
INFO [2025-08-22 19:54:42] [1] "black"
INFO [2025-08-22 19:54:42] 
INFO [2025-08-22 19:54:42] $cat.fontface
INFO [2025-08-22 19:54:42] [1] "plain"
INFO [2025-08-22 19:54:42] 
INFO [2025-08-22 19:54:42] $cat.fontfamily
INFO [2025-08-22 19:54:42] [1] "serif"
INFO [2025-08-22 19:54:42] 
INFO [2025-08-22 19:54:42] $x
INFO [2025-08-22 19:54:42] $x$TF1
INFO [2025-08-22 19:54:42] [1] 1 2 3
INFO [2025-08-22 19:54:42] 
INFO [2025-08-22 19:54:42] $x$TF2
INFO [2025-08-22 19:54:42] [1] 1 2 3
INFO [2025-08-22 19:54:42] 
INFO [2025-08-22 19:54:42] 
INFO [2025-08-22 19:54:42] $disable.logging
INFO [2025-08-22 19:54:42] [1] TRUE
INFO [2025-08-22 19:54:42] 
INFO [2025-08-22 19:54:42] $filename
INFO [2025-08-22 19:54:42] NULL
INFO [2025-08-22 19:54:42] 
INFO [2025-08-22 19:54:42] $scaled
INFO [2025-08-22 19:54:42] [1] FALSE
INFO [2025-08-22 19:54:42] 
INFO [2025-08-22 19:54:42] $euler.d
INFO [2025-08-22 19:54:42] [1] FALSE
INFO [2025-08-22 19:54:42] 
INFO [2025-08-22 19:54:42] $cat.cex
INFO [2025-08-22 19:54:42] [1] 1
INFO [2025-08-22 19:54:42] 
INFO [2025-08-22 19:54:42] $cat.col
INFO [2025-08-22 19:54:42] [1] "black"
INFO [2025-08-22 19:54:42] 
INFO [2025-08-22 19:54:42] $cat.fontface
INFO [2025-08-22 19:54:42] [1] "plain"
INFO [2025-08-22 19:54:42] 
INFO [2025-08-22 19:54:42] $cat.fontfamily
INFO [2025-08-22 19:54:42] [1] "serif"
INFO [2025-08-22 19:54:42] 
INFO [2025-08-22 19:54:42] $x
INFO [2025-08-22 19:54:42] $x$TF1
INFO [2025-08-22 19:54:42] [1] 4 5 6
INFO [2025-08-22 19:54:42] 
INFO [2025-08-22 19:54:42] $x$TF2
INFO [2025-08-22 19:54:42] [1] 1 2 3
INFO [2025-08-22 19:54:42] 
INFO [2025-08-22 19:54:42] 
INFO [2025-08-22 19:54:42] $disable.logging
INFO [2025-08-22 19:54:42] [1] TRUE
INFO [2025-08-22 19:54:42] 
INFO [2025-08-22 19:54:42] $filename
INFO [2025-08-22 19:54:42] NULL
INFO [2025-08-22 19:54:42] 
INFO [2025-08-22 19:54:43] $scaled
INFO [2025-08-22 19:54:43] [1] FALSE
INFO [2025-08-22 19:54:43] 
INFO [2025-08-22 19:54:43] $euler.d
INFO [2025-08-22 19:54:43] [1] FALSE
INFO [2025-08-22 19:54:43] 
INFO [2025-08-22 19:54:43] $cat.cex
INFO [2025-08-22 19:54:43] [1] 1
INFO [2025-08-22 19:54:43] 
INFO [2025-08-22 19:54:43] $cat.col
INFO [2025-08-22 19:54:43] [1] "black"
INFO [2025-08-22 19:54:43] 
INFO [2025-08-22 19:54:43] $cat.fontface
INFO [2025-08-22 19:54:43] [1] "plain"
INFO [2025-08-22 19:54:43] 
INFO [2025-08-22 19:54:43] $cat.fontfamily
INFO [2025-08-22 19:54:43] [1] "serif"
INFO [2025-08-22 19:54:43] 
INFO [2025-08-22 19:54:43] $x
INFO [2025-08-22 19:54:43] $x$TF1
INFO [2025-08-22 19:54:43] [1] 4 5 6
INFO [2025-08-22 19:54:43] 
INFO [2025-08-22 19:54:43] $x$TF2
INFO [2025-08-22 19:54:43] [1] 1 2 3
INFO [2025-08-22 19:54:43] 
INFO [2025-08-22 19:54:43] 
INFO [2025-08-22 19:54:43] $disable.logging
INFO [2025-08-22 19:54:43] [1] TRUE
INFO [2025-08-22 19:54:43] 
INFO [2025-08-22 19:54:43] $filename
INFO [2025-08-22 19:54:43] NULL
INFO [2025-08-22 19:54:43] 
INFO [2025-08-22 19:54:43] $scaled
INFO [2025-08-22 19:54:43] [1] FALSE
INFO [2025-08-22 19:54:43] 
INFO [2025-08-22 19:54:43] $euler.d
INFO [2025-08-22 19:54:43] [1] FALSE
INFO [2025-08-22 19:54:43] 
INFO [2025-08-22 19:54:43] $cat.cex
INFO [2025-08-22 19:54:43] [1] 1
INFO [2025-08-22 19:54:43] 
INFO [2025-08-22 19:54:43] $cat.col
INFO [2025-08-22 19:54:43] [1] "black"
INFO [2025-08-22 19:54:43] 
INFO [2025-08-22 19:54:43] $cat.fontface
INFO [2025-08-22 19:54:43] [1] "plain"
INFO [2025-08-22 19:54:43] 
INFO [2025-08-22 19:54:43] $cat.fontfamily
INFO [2025-08-22 19:54:43] [1] "serif"
INFO [2025-08-22 19:54:43] 
INFO [2025-08-22 19:54:43] $x
INFO [2025-08-22 19:54:43] $x$TF1
INFO [2025-08-22 19:54:43] [1] 4 5 6
INFO [2025-08-22 19:54:43] 
INFO [2025-08-22 19:54:43] $x$TF2
INFO [2025-08-22 19:54:43] [1] 1 2 3
INFO [2025-08-22 19:54:43] 
INFO [2025-08-22 19:54:43] $x$TF3
INFO [2025-08-22 19:54:43] [1] 2 3 6
INFO [2025-08-22 19:54:43] 
INFO [2025-08-22 19:54:43] 
INFO [2025-08-22 19:54:43] $disable.logging
INFO [2025-08-22 19:54:43] [1] TRUE
INFO [2025-08-22 19:54:43] 
INFO [2025-08-22 19:54:43] $filename
INFO [2025-08-22 19:54:43] NULL
INFO [2025-08-22 19:54:43] 
INFO [2025-08-22 19:54:43] $scaled
INFO [2025-08-22 19:54:43] [1] FALSE
INFO [2025-08-22 19:54:43] 
INFO [2025-08-22 19:54:43] $euler.d
INFO [2025-08-22 19:54:43] [1] FALSE
INFO [2025-08-22 19:54:43] 
INFO [2025-08-22 19:54:43] $cat.cex
INFO [2025-08-22 19:54:43] [1] 1
INFO [2025-08-22 19:54:43] 
INFO [2025-08-22 19:54:43] $cat.col
INFO [2025-08-22 19:54:43] [1] "black"
INFO [2025-08-22 19:54:43] 
INFO [2025-08-22 19:54:43] $cat.fontface
INFO [2025-08-22 19:54:43] [1] "plain"
INFO [2025-08-22 19:54:43] 
INFO [2025-08-22 19:54:43] $cat.fontfamily
INFO [2025-08-22 19:54:43] [1] "serif"
INFO [2025-08-22 19:54:43] 
INFO [2025-08-22 19:54:43] $x
INFO [2025-08-22 19:54:43] $x$TF1
INFO [2025-08-22 19:54:43] [1] 3 4 5
INFO [2025-08-22 19:54:43] 
INFO [2025-08-22 19:54:43] $x$TF2
INFO [2025-08-22 19:54:43] [1] 1 2 5
INFO [2025-08-22 19:54:43] 
INFO [2025-08-22 19:54:43] $x$TF3
INFO [2025-08-22 19:54:43] [1] 1 2 5
INFO [2025-08-22 19:54:43] 
INFO [2025-08-22 19:54:43] 
INFO [2025-08-22 19:54:43] $disable.logging
INFO [2025-08-22 19:54:43] [1] TRUE
INFO [2025-08-22 19:54:43] 
INFO [2025-08-22 19:54:43] $filename
INFO [2025-08-22 19:54:43] NULL
INFO [2025-08-22 19:54:43] 
INFO [2025-08-22 19:54:44] $scaled
INFO [2025-08-22 19:54:44] [1] FALSE
INFO [2025-08-22 19:54:44] 
INFO [2025-08-22 19:54:44] $euler.d
INFO [2025-08-22 19:54:44] [1] FALSE
INFO [2025-08-22 19:54:44] 
INFO [2025-08-22 19:54:44] $cat.cex
INFO [2025-08-22 19:54:44] [1] 1
INFO [2025-08-22 19:54:44] 
INFO [2025-08-22 19:54:44] $cat.col
INFO [2025-08-22 19:54:44] [1] "black"
INFO [2025-08-22 19:54:44] 
INFO [2025-08-22 19:54:44] $cat.fontface
INFO [2025-08-22 19:54:44] [1] "plain"
INFO [2025-08-22 19:54:44] 
INFO [2025-08-22 19:54:44] $cat.fontfamily
INFO [2025-08-22 19:54:44] [1] "serif"
INFO [2025-08-22 19:54:44] 
INFO [2025-08-22 19:54:44] $x
INFO [2025-08-22 19:54:44] $x$TF1
INFO [2025-08-22 19:54:44] [1] 3 4 5
INFO [2025-08-22 19:54:44] 
INFO [2025-08-22 19:54:44] $x$TF2
INFO [2025-08-22 19:54:44] [1] 1 2 5
INFO [2025-08-22 19:54:44] 
INFO [2025-08-22 19:54:44] $x$TF3
INFO [2025-08-22 19:54:44] [1] 1 2 5
INFO [2025-08-22 19:54:44] 
INFO [2025-08-22 19:54:44] $x$TF4
INFO [2025-08-22 19:54:44] [1] 1 2 5
INFO [2025-08-22 19:54:44] 
INFO [2025-08-22 19:54:44] 
INFO [2025-08-22 19:54:44] $disable.logging
INFO [2025-08-22 19:54:44] [1] TRUE
INFO [2025-08-22 19:54:44] 
INFO [2025-08-22 19:54:44] $filename
INFO [2025-08-22 19:54:44] NULL
INFO [2025-08-22 19:54:44] 
[ 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 
219.417   6.740 228.824 

Example timings

ChIPpeakAnno.Rcheck/ChIPpeakAnno-Ex.timings

nameusersystemelapsed
ChIPpeakAnno-package0.0000.0000.001
ExonPlusUtr.human.GRCh373.3420.1023.460
HOT.spots0.0930.0080.102
IDRfilter0.0010.0000.002
Peaks.Ste12.Replicate10.0570.0030.060
Peaks.Ste12.Replicate20.0130.0020.016
Peaks.Ste12.Replicate30.0150.0020.017
TSS.human.GRCh370.1610.0080.170
TSS.human.GRCh380.1330.0080.142
TSS.human.NCBI360.0930.0060.101
TSS.mouse.GRCm380.0850.0050.090
TSS.mouse.NCBIM370.0800.0050.086
TSS.rat.RGSC3.40.0680.0040.073
TSS.rat.Rnor_5.00.0560.0040.060
TSS.zebrafish.Zv80.0620.0050.068
TSS.zebrafish.Zv90.0810.0070.088
addAncestors1.2470.1031.387
addGeneIDs2.4240.9783.436
addMetadata1.4620.0711.540
annoGR0.0010.0010.001
annoPeaks3.0840.3223.453
annotatePeakInBatch14.137 0.80615.049
annotatedPeak0.0540.0040.057
assignChromosomeRegion0.0020.0010.002
bdp0.0000.0000.001
binOverFeature0.9260.0340.969
binOverGene0.0010.0010.001
binOverRegions0.0000.0010.001
condenseMatrixByColnames0.0150.0010.016
convert2EntrezID0.4990.0080.509
countPatternInSeqs0.1710.0070.182
cumulativePercentage000
downstreams0.0280.0000.028
egOrgMap000
enrichedGO0.0020.0030.005
enrichmentPlot0.5390.0100.552
estFragmentLength0.0010.0000.001
estLibSize0.0010.0010.001
featureAlignedDistribution0.2420.0020.245
featureAlignedExtendSignal0.0020.0000.002
featureAlignedHeatmap0.4230.0100.435
featureAlignedSignal0.2000.0450.245
findEnhancers27.882 0.92928.982
findMotifsInPromoterSeqs17.545 0.45918.303
findOverlappingPeaks0.0010.0000.001
findOverlapsOfPeaks2.1940.0282.233
genomicElementDistribution0.0020.0010.003
genomicElementUpSetR0.0010.0010.001
getAllPeakSequence0.6190.0270.653
getAnnotation0.0010.0000.002
getEnrichedGO0.0090.0050.014
getEnrichedPATH0.0000.0000.001
getGO0.0000.0000.001
getGeneSeq0.0020.0010.001
getUniqueGOidCount0.0010.0010.001
getVennCounts0.0010.0000.002
hyperGtest0.0020.0000.002
makeVennDiagram0.0040.0000.004
mergePlusMinusPeaks0.0000.0000.001
metagenePlot2.4640.0662.542
myPeakList0.0140.0030.017
oligoFrequency0.1340.0080.142
oligoSummary0.0010.0010.001
peakPermTest0.0020.0000.002
peaks10.0090.0020.011
peaks20.0100.0020.013
peaks30.0100.0030.013
peaksNearBDP0.0010.0000.001
pie10.0060.0010.007
plotBinOverRegions0.0010.0010.001
preparePool0.0010.0000.000
reCenterPeaks0.0330.0000.033
summarizeOverlapsByBins5.6140.4865.802
summarizePatternInPeaks1.7220.2321.968
tileCount0.4350.3660.497
tileGRanges0.0470.0140.062
toGRanges0.1080.0130.121
translatePattern0.0010.0000.001
wgEncodeTfbsV30.1590.0140.173
write2FASTA0.0170.0020.019
xget0.1420.0120.155