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This page was generated on 2025-09-20 12:04 -0400 (Sat, 20 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4814
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4603
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4547
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4553
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 344/2333HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPpeakAnno 3.43.1  (landing page)
Jianhong Ou
Snapshot Date: 2025-09-19 13:45 -0400 (Fri, 19 Sep 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: 2025-09-19 19:55:25 -0400 (Fri, 19 Sep 2025)
EndedAt: 2025-09-19 20:07:28 -0400 (Fri, 19 Sep 2025)
EllapsedTime: 722.6 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 Patched (2025-09-10 r88807)
* 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 21.6Mb
  sub-directories of 1Mb or more:
    R         1.0Mb
    data     13.1Mb
    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            28.061  0.982  29.221
findMotifsInPromoterSeqs 17.716  0.640  18.814
annotatePeakInBatch      13.833  0.790  14.739
summarizeOverlapsByBins   5.924  0.528   6.129
* 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 Patched (2025-09-10 r88807) -- "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 [2025-09-19 20:06:58] $cat.cex
INFO [2025-09-19 20:06:58] [1] 1
INFO [2025-09-19 20:06:58] 
INFO [2025-09-19 20:06:58] $cat.col
INFO [2025-09-19 20:06:58] [1] "black"
INFO [2025-09-19 20:06:58] 
INFO [2025-09-19 20:06:58] $cat.fontface
INFO [2025-09-19 20:06:58] [1] "plain"
INFO [2025-09-19 20:06:58] 
INFO [2025-09-19 20:06:58] $cat.fontfamily
INFO [2025-09-19 20:06:58] [1] "serif"
INFO [2025-09-19 20:06:58] 
INFO [2025-09-19 20:06:58] $x
INFO [2025-09-19 20:06:58] $x$TF1
INFO [2025-09-19 20:06:58] [1] 3 4 5
INFO [2025-09-19 20:06:58] 
INFO [2025-09-19 20:06:58] $x$TF2
INFO [2025-09-19 20:06:58] [1] 1 2 3 4 5
INFO [2025-09-19 20:06:58] 
INFO [2025-09-19 20:06:58] 
INFO [2025-09-19 20:06:58] $disable.logging
INFO [2025-09-19 20:06:58] [1] TRUE
INFO [2025-09-19 20:06:58] 
INFO [2025-09-19 20:06:58] $filename
INFO [2025-09-19 20:06:58] NULL
INFO [2025-09-19 20:06:58] 
INFO [2025-09-19 20:06:58] $cat.cex
INFO [2025-09-19 20:06:58] [1] 1
INFO [2025-09-19 20:06:58] 
INFO [2025-09-19 20:06:58] $cat.col
INFO [2025-09-19 20:06:58] [1] "black"
INFO [2025-09-19 20:06:58] 
INFO [2025-09-19 20:06:58] $cat.fontface
INFO [2025-09-19 20:06:58] [1] "plain"
INFO [2025-09-19 20:06:58] 
INFO [2025-09-19 20:06:58] $cat.fontfamily
INFO [2025-09-19 20:06:58] [1] "serif"
INFO [2025-09-19 20:06:58] 
INFO [2025-09-19 20:06:58] $x
INFO [2025-09-19 20:06:58] $x$TF1
INFO [2025-09-19 20:06:58] [1] 3 4 5
INFO [2025-09-19 20:06:58] 
INFO [2025-09-19 20:06:58] $x$TF2
INFO [2025-09-19 20:06:58] [1] 1 2 4 5
INFO [2025-09-19 20:06:58] 
INFO [2025-09-19 20:06:58] $x$TF3
INFO [2025-09-19 20:06:58] [1] 3 4 5
INFO [2025-09-19 20:06:58] 
INFO [2025-09-19 20:06:58] $x$TF4
INFO [2025-09-19 20:06:58] [1] 1 2 4 5
INFO [2025-09-19 20:06:58] 
INFO [2025-09-19 20:06:58] 
INFO [2025-09-19 20:06:58] $disable.logging
INFO [2025-09-19 20:06:58] [1] TRUE
INFO [2025-09-19 20:06:58] 
INFO [2025-09-19 20:06:58] $filename
INFO [2025-09-19 20:06:58] NULL
INFO [2025-09-19 20:06:58] 
INFO [2025-09-19 20:06:59] $scaled
INFO [2025-09-19 20:06:59] [1] FALSE
INFO [2025-09-19 20:06:59] 
INFO [2025-09-19 20:06:59] $euler.d
INFO [2025-09-19 20:06:59] [1] FALSE
INFO [2025-09-19 20:06:59] 
INFO [2025-09-19 20:06:59] $cat.cex
INFO [2025-09-19 20:06:59] [1] 1
INFO [2025-09-19 20:06:59] 
INFO [2025-09-19 20:06:59] $cat.col
INFO [2025-09-19 20:06:59] [1] "black"
INFO [2025-09-19 20:06:59] 
INFO [2025-09-19 20:06:59] $cat.fontface
INFO [2025-09-19 20:06:59] [1] "plain"
INFO [2025-09-19 20:06:59] 
INFO [2025-09-19 20:06:59] $cat.fontfamily
INFO [2025-09-19 20:06:59] [1] "serif"
INFO [2025-09-19 20:06:59] 
INFO [2025-09-19 20:06:59] $x
INFO [2025-09-19 20:06:59] $x$TF1
INFO [2025-09-19 20:06:59] [1] 1 2 3
INFO [2025-09-19 20:06:59] 
INFO [2025-09-19 20:06:59] $x$TF2
INFO [2025-09-19 20:06:59] [1] 1 2 3
INFO [2025-09-19 20:06:59] 
INFO [2025-09-19 20:06:59] 
INFO [2025-09-19 20:06:59] $disable.logging
INFO [2025-09-19 20:06:59] [1] TRUE
INFO [2025-09-19 20:06:59] 
INFO [2025-09-19 20:06:59] $filename
INFO [2025-09-19 20:06:59] NULL
INFO [2025-09-19 20:06:59] 
INFO [2025-09-19 20:06:59] $scaled
INFO [2025-09-19 20:06:59] [1] FALSE
INFO [2025-09-19 20:06:59] 
INFO [2025-09-19 20:06:59] $euler.d
INFO [2025-09-19 20:06:59] [1] FALSE
INFO [2025-09-19 20:06:59] 
INFO [2025-09-19 20:06:59] $cat.cex
INFO [2025-09-19 20:06:59] [1] 1
INFO [2025-09-19 20:06:59] 
INFO [2025-09-19 20:06:59] $cat.col
INFO [2025-09-19 20:06:59] [1] "black"
INFO [2025-09-19 20:06:59] 
INFO [2025-09-19 20:06:59] $cat.fontface
INFO [2025-09-19 20:06:59] [1] "plain"
INFO [2025-09-19 20:06:59] 
INFO [2025-09-19 20:06:59] $cat.fontfamily
INFO [2025-09-19 20:06:59] [1] "serif"
INFO [2025-09-19 20:06:59] 
INFO [2025-09-19 20:06:59] $x
INFO [2025-09-19 20:06:59] $x$TF1
INFO [2025-09-19 20:06:59] [1] 4 5 6
INFO [2025-09-19 20:06:59] 
INFO [2025-09-19 20:06:59] $x$TF2
INFO [2025-09-19 20:06:59] [1] 1 2 3
INFO [2025-09-19 20:06:59] 
INFO [2025-09-19 20:06:59] 
INFO [2025-09-19 20:06:59] $disable.logging
INFO [2025-09-19 20:06:59] [1] TRUE
INFO [2025-09-19 20:06:59] 
INFO [2025-09-19 20:06:59] $filename
INFO [2025-09-19 20:06:59] NULL
INFO [2025-09-19 20:06:59] 
INFO [2025-09-19 20:06:59] $scaled
INFO [2025-09-19 20:06:59] [1] FALSE
INFO [2025-09-19 20:06:59] 
INFO [2025-09-19 20:06:59] $euler.d
INFO [2025-09-19 20:06:59] [1] FALSE
INFO [2025-09-19 20:06:59] 
INFO [2025-09-19 20:06:59] $cat.cex
INFO [2025-09-19 20:06:59] [1] 1
INFO [2025-09-19 20:06:59] 
INFO [2025-09-19 20:06:59] $cat.col
INFO [2025-09-19 20:06:59] [1] "black"
INFO [2025-09-19 20:06:59] 
INFO [2025-09-19 20:06:59] $cat.fontface
INFO [2025-09-19 20:06:59] [1] "plain"
INFO [2025-09-19 20:06:59] 
INFO [2025-09-19 20:06:59] $cat.fontfamily
INFO [2025-09-19 20:06:59] [1] "serif"
INFO [2025-09-19 20:06:59] 
INFO [2025-09-19 20:06:59] $x
INFO [2025-09-19 20:06:59] $x$TF1
INFO [2025-09-19 20:06:59] [1] 4 5 6
INFO [2025-09-19 20:06:59] 
INFO [2025-09-19 20:06:59] $x$TF2
INFO [2025-09-19 20:06:59] [1] 1 2 3
INFO [2025-09-19 20:06:59] 
INFO [2025-09-19 20:06:59] 
INFO [2025-09-19 20:06:59] $disable.logging
INFO [2025-09-19 20:06:59] [1] TRUE
INFO [2025-09-19 20:06:59] 
INFO [2025-09-19 20:06:59] $filename
INFO [2025-09-19 20:06:59] NULL
INFO [2025-09-19 20:06:59] 
INFO [2025-09-19 20:07:00] $scaled
INFO [2025-09-19 20:07:00] [1] FALSE
INFO [2025-09-19 20:07:00] 
INFO [2025-09-19 20:07:00] $euler.d
INFO [2025-09-19 20:07:00] [1] FALSE
INFO [2025-09-19 20:07:00] 
INFO [2025-09-19 20:07:00] $cat.cex
INFO [2025-09-19 20:07:00] [1] 1
INFO [2025-09-19 20:07:00] 
INFO [2025-09-19 20:07:00] $cat.col
INFO [2025-09-19 20:07:00] [1] "black"
INFO [2025-09-19 20:07:00] 
INFO [2025-09-19 20:07:00] $cat.fontface
INFO [2025-09-19 20:07:00] [1] "plain"
INFO [2025-09-19 20:07:00] 
INFO [2025-09-19 20:07:00] $cat.fontfamily
INFO [2025-09-19 20:07:00] [1] "serif"
INFO [2025-09-19 20:07:00] 
INFO [2025-09-19 20:07:00] $x
INFO [2025-09-19 20:07:00] $x$TF1
INFO [2025-09-19 20:07:00] [1] 4 5 6
INFO [2025-09-19 20:07:00] 
INFO [2025-09-19 20:07:00] $x$TF2
INFO [2025-09-19 20:07:00] [1] 1 2 3
INFO [2025-09-19 20:07:00] 
INFO [2025-09-19 20:07:00] $x$TF3
INFO [2025-09-19 20:07:00] [1] 2 3 6
INFO [2025-09-19 20:07:00] 
INFO [2025-09-19 20:07:00] 
INFO [2025-09-19 20:07:00] $disable.logging
INFO [2025-09-19 20:07:00] [1] TRUE
INFO [2025-09-19 20:07:00] 
INFO [2025-09-19 20:07:00] $filename
INFO [2025-09-19 20:07:00] NULL
INFO [2025-09-19 20:07:00] 
INFO [2025-09-19 20:07:00] $scaled
INFO [2025-09-19 20:07:00] [1] FALSE
INFO [2025-09-19 20:07:00] 
INFO [2025-09-19 20:07:00] $euler.d
INFO [2025-09-19 20:07:00] [1] FALSE
INFO [2025-09-19 20:07:00] 
INFO [2025-09-19 20:07:00] $cat.cex
INFO [2025-09-19 20:07:00] [1] 1
INFO [2025-09-19 20:07:00] 
INFO [2025-09-19 20:07:00] $cat.col
INFO [2025-09-19 20:07:00] [1] "black"
INFO [2025-09-19 20:07:00] 
INFO [2025-09-19 20:07:00] $cat.fontface
INFO [2025-09-19 20:07:00] [1] "plain"
INFO [2025-09-19 20:07:00] 
INFO [2025-09-19 20:07:00] $cat.fontfamily
INFO [2025-09-19 20:07:00] [1] "serif"
INFO [2025-09-19 20:07:00] 
INFO [2025-09-19 20:07:00] $x
INFO [2025-09-19 20:07:00] $x$TF1
INFO [2025-09-19 20:07:00] [1] 3 4 5
INFO [2025-09-19 20:07:00] 
INFO [2025-09-19 20:07:00] $x$TF2
INFO [2025-09-19 20:07:00] [1] 1 2 5
INFO [2025-09-19 20:07:00] 
INFO [2025-09-19 20:07:00] $x$TF3
INFO [2025-09-19 20:07:00] [1] 1 2 5
INFO [2025-09-19 20:07:00] 
INFO [2025-09-19 20:07:00] 
INFO [2025-09-19 20:07:00] $disable.logging
INFO [2025-09-19 20:07:00] [1] TRUE
INFO [2025-09-19 20:07:00] 
INFO [2025-09-19 20:07:00] $filename
INFO [2025-09-19 20:07:00] NULL
INFO [2025-09-19 20:07:00] 
INFO [2025-09-19 20:07:01] $scaled
INFO [2025-09-19 20:07:01] [1] FALSE
INFO [2025-09-19 20:07:01] 
INFO [2025-09-19 20:07:01] $euler.d
INFO [2025-09-19 20:07:01] [1] FALSE
INFO [2025-09-19 20:07:01] 
INFO [2025-09-19 20:07:01] $cat.cex
INFO [2025-09-19 20:07:01] [1] 1
INFO [2025-09-19 20:07:01] 
INFO [2025-09-19 20:07:01] $cat.col
INFO [2025-09-19 20:07:01] [1] "black"
INFO [2025-09-19 20:07:01] 
INFO [2025-09-19 20:07:01] $cat.fontface
INFO [2025-09-19 20:07:01] [1] "plain"
INFO [2025-09-19 20:07:01] 
INFO [2025-09-19 20:07:01] $cat.fontfamily
INFO [2025-09-19 20:07:01] [1] "serif"
INFO [2025-09-19 20:07:01] 
INFO [2025-09-19 20:07:01] $x
INFO [2025-09-19 20:07:01] $x$TF1
INFO [2025-09-19 20:07:01] [1] 3 4 5
INFO [2025-09-19 20:07:01] 
INFO [2025-09-19 20:07:01] $x$TF2
INFO [2025-09-19 20:07:01] [1] 1 2 5
INFO [2025-09-19 20:07:01] 
INFO [2025-09-19 20:07:01] $x$TF3
INFO [2025-09-19 20:07:01] [1] 1 2 5
INFO [2025-09-19 20:07:01] 
INFO [2025-09-19 20:07:01] $x$TF4
INFO [2025-09-19 20:07:01] [1] 1 2 5
INFO [2025-09-19 20:07:01] 
INFO [2025-09-19 20:07:01] 
INFO [2025-09-19 20:07:01] $disable.logging
INFO [2025-09-19 20:07:01] [1] TRUE
INFO [2025-09-19 20:07:01] 
INFO [2025-09-19 20:07:01] $filename
INFO [2025-09-19 20:07:01] NULL
INFO [2025-09-19 20:07:01] 
[ 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 
219.025   6.959 228.667 

Example timings

ChIPpeakAnno.Rcheck/ChIPpeakAnno-Ex.timings

nameusersystemelapsed
ChIPpeakAnno-package0.0010.0000.000
ExonPlusUtr.human.GRCh373.3940.1023.513
HOT.spots0.0960.0070.104
IDRfilter0.0010.0000.002
Peaks.Ste12.Replicate10.0530.0030.057
Peaks.Ste12.Replicate20.0120.0030.015
Peaks.Ste12.Replicate30.0110.0030.014
TSS.human.GRCh370.0860.0040.090
TSS.human.GRCh380.2000.0130.214
TSS.human.NCBI360.0920.0060.098
TSS.mouse.GRCm380.0840.0060.091
TSS.mouse.NCBIM370.0770.0050.082
TSS.rat.RGSC3.40.0660.0050.071
TSS.rat.Rnor_5.00.0500.0040.054
TSS.zebrafish.Zv80.0560.0050.061
TSS.zebrafish.Zv90.0700.0060.075
addAncestors1.1910.0941.323
addGeneIDs2.6120.9733.619
addMetadata1.2590.1091.375
annoGR0.0000.0010.001
annoPeaks3.3550.3243.743
annotatePeakInBatch13.833 0.79014.739
annotatedPeak0.0440.0030.048
assignChromosomeRegion0.0010.0010.002
bdp000
binOverFeature0.7680.0320.807
binOverGene0.0010.0000.001
binOverRegions0.0010.0000.001
condenseMatrixByColnames0.0100.0010.010
convert2EntrezID0.4510.0070.461
countPatternInSeqs0.1640.0070.174
cumulativePercentage0.0010.0000.000
downstreams0.0250.0010.026
egOrgMap000
enrichedGO0.0020.0020.004
enrichmentPlot0.7100.0120.727
estFragmentLength0.0010.0000.001
estLibSize0.0010.0000.000
featureAlignedDistribution0.3390.0080.352
featureAlignedExtendSignal0.0020.0000.002
featureAlignedHeatmap0.3330.0030.337
featureAlignedSignal0.2050.0720.280
findEnhancers28.061 0.98229.221
findMotifsInPromoterSeqs17.716 0.64018.814
findOverlappingPeaks0.0010.0000.002
findOverlapsOfPeaks2.0980.0262.136
genomicElementDistribution0.0020.0000.002
genomicElementUpSetR0.0010.0000.001
getAllPeakSequence0.6000.0250.630
getAnnotation0.0020.0000.002
getEnrichedGO0.0110.0060.017
getEnrichedPATH0.0010.0000.002
getGO000
getGeneSeq0.0020.0010.002
getUniqueGOidCount0.0010.0010.001
getVennCounts0.0020.0000.002
hyperGtest0.0020.0000.002
makeVennDiagram0.0050.0000.005
mergePlusMinusPeaks0.0010.0000.001
metagenePlot2.8480.1042.969
myPeakList0.0130.0020.016
oligoFrequency0.1340.0080.142
oligoSummary0.0010.0000.001
peakPermTest0.0020.0000.002
peaks10.0080.0020.011
peaks20.0080.0020.011
peaks30.0070.0020.009
peaksNearBDP0.0010.0000.002
pie10.0070.0010.008
plotBinOverRegions0.0000.0000.002
preparePool0.0010.0000.001
reCenterPeaks0.0300.0000.031
summarizeOverlapsByBins5.9240.5286.129
summarizePatternInPeaks1.7070.2321.969
tileCount0.4380.3920.513
tileGRanges0.0500.0120.062
toGRanges0.0970.0130.111
translatePattern0.0000.0010.000
wgEncodeTfbsV30.1490.0150.164
write2FASTA0.0210.0040.026
xget0.1420.0140.156