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This page was generated on 2025-10-16 11:40 -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 kjohnson1

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: /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_3.42.0.tar.gz
StartedAt: 2025-10-14 15:54:31 -0400 (Tue, 14 Oct 2025)
EndedAt: 2025-10-14 16:06:35 -0400 (Tue, 14 Oct 2025)
EllapsedTime: 724.5 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_3.42.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/ChIPpeakAnno.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChIPpeakAnno/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChIPpeakAnno’ version ‘3.42.0’
* 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 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            24.407  0.586  25.353
findMotifsInPromoterSeqs 17.325  0.542  18.291
annotatePeakInBatch      14.087  0.630  14.939
summarizeOverlapsByBins   7.200  0.507   7.475
ExonPlusUtr.human.GRCh37  5.008  0.150   5.241
annoPeaks                 3.498  0.294   5.990
* 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-arm64/Resources/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 Patched (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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: 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 [2025-10-14 16:06:05] $cat.cex
INFO [2025-10-14 16:06:05] [1] 1
INFO [2025-10-14 16:06:05] 
INFO [2025-10-14 16:06:05] $cat.col
INFO [2025-10-14 16:06:05] [1] "black"
INFO [2025-10-14 16:06:05] 
INFO [2025-10-14 16:06:05] $cat.fontface
INFO [2025-10-14 16:06:05] [1] "plain"
INFO [2025-10-14 16:06:05] 
INFO [2025-10-14 16:06:05] $cat.fontfamily
INFO [2025-10-14 16:06:05] [1] "serif"
INFO [2025-10-14 16:06:05] 
INFO [2025-10-14 16:06:05] $x
INFO [2025-10-14 16:06:05] $x$TF1
INFO [2025-10-14 16:06:05] [1] 3 4 5
INFO [2025-10-14 16:06:05] 
INFO [2025-10-14 16:06:05] $x$TF2
INFO [2025-10-14 16:06:05] [1] 1 2 3 4 5
INFO [2025-10-14 16:06:05] 
INFO [2025-10-14 16:06:05] 
INFO [2025-10-14 16:06:05] $disable.logging
INFO [2025-10-14 16:06:05] [1] TRUE
INFO [2025-10-14 16:06:05] 
INFO [2025-10-14 16:06:05] $filename
INFO [2025-10-14 16:06:05] NULL
INFO [2025-10-14 16:06:05] 
INFO [2025-10-14 16:06:05] $cat.cex
INFO [2025-10-14 16:06:05] [1] 1
INFO [2025-10-14 16:06:05] 
INFO [2025-10-14 16:06:05] $cat.col
INFO [2025-10-14 16:06:05] [1] "black"
INFO [2025-10-14 16:06:05] 
INFO [2025-10-14 16:06:05] $cat.fontface
INFO [2025-10-14 16:06:05] [1] "plain"
INFO [2025-10-14 16:06:05] 
INFO [2025-10-14 16:06:05] $cat.fontfamily
INFO [2025-10-14 16:06:05] [1] "serif"
INFO [2025-10-14 16:06:05] 
INFO [2025-10-14 16:06:05] $x
INFO [2025-10-14 16:06:05] $x$TF1
INFO [2025-10-14 16:06:05] [1] 3 4 5
INFO [2025-10-14 16:06:05] 
INFO [2025-10-14 16:06:05] $x$TF2
INFO [2025-10-14 16:06:05] [1] 1 2 4 5
INFO [2025-10-14 16:06:05] 
INFO [2025-10-14 16:06:05] $x$TF3
INFO [2025-10-14 16:06:05] [1] 3 4 5
INFO [2025-10-14 16:06:05] 
INFO [2025-10-14 16:06:05] $x$TF4
INFO [2025-10-14 16:06:05] [1] 1 2 4 5
INFO [2025-10-14 16:06:05] 
INFO [2025-10-14 16:06:05] 
INFO [2025-10-14 16:06:05] $disable.logging
INFO [2025-10-14 16:06:05] [1] TRUE
INFO [2025-10-14 16:06:05] 
INFO [2025-10-14 16:06:05] $filename
INFO [2025-10-14 16:06:05] NULL
INFO [2025-10-14 16:06:05] 
INFO [2025-10-14 16:06:06] $scaled
INFO [2025-10-14 16:06:06] [1] FALSE
INFO [2025-10-14 16:06:06] 
INFO [2025-10-14 16:06:06] $euler.d
INFO [2025-10-14 16:06:06] [1] FALSE
INFO [2025-10-14 16:06:06] 
INFO [2025-10-14 16:06:06] $cat.cex
INFO [2025-10-14 16:06:06] [1] 1
INFO [2025-10-14 16:06:06] 
INFO [2025-10-14 16:06:06] $cat.col
INFO [2025-10-14 16:06:06] [1] "black"
INFO [2025-10-14 16:06:06] 
INFO [2025-10-14 16:06:06] $cat.fontface
INFO [2025-10-14 16:06:06] [1] "plain"
INFO [2025-10-14 16:06:06] 
INFO [2025-10-14 16:06:06] $cat.fontfamily
INFO [2025-10-14 16:06:06] [1] "serif"
INFO [2025-10-14 16:06:06] 
INFO [2025-10-14 16:06:06] $x
INFO [2025-10-14 16:06:06] $x$TF1
INFO [2025-10-14 16:06:06] [1] 1 2 3
INFO [2025-10-14 16:06:06] 
INFO [2025-10-14 16:06:06] $x$TF2
INFO [2025-10-14 16:06:06] [1] 1 2 3
INFO [2025-10-14 16:06:06] 
INFO [2025-10-14 16:06:06] 
INFO [2025-10-14 16:06:06] $disable.logging
INFO [2025-10-14 16:06:06] [1] TRUE
INFO [2025-10-14 16:06:06] 
INFO [2025-10-14 16:06:06] $filename
INFO [2025-10-14 16:06:06] NULL
INFO [2025-10-14 16:06:06] 
INFO [2025-10-14 16:06:06] $scaled
INFO [2025-10-14 16:06:06] [1] FALSE
INFO [2025-10-14 16:06:06] 
INFO [2025-10-14 16:06:06] $euler.d
INFO [2025-10-14 16:06:06] [1] FALSE
INFO [2025-10-14 16:06:06] 
INFO [2025-10-14 16:06:06] $cat.cex
INFO [2025-10-14 16:06:06] [1] 1
INFO [2025-10-14 16:06:06] 
INFO [2025-10-14 16:06:06] $cat.col
INFO [2025-10-14 16:06:06] [1] "black"
INFO [2025-10-14 16:06:06] 
INFO [2025-10-14 16:06:06] $cat.fontface
INFO [2025-10-14 16:06:06] [1] "plain"
INFO [2025-10-14 16:06:06] 
INFO [2025-10-14 16:06:06] $cat.fontfamily
INFO [2025-10-14 16:06:06] [1] "serif"
INFO [2025-10-14 16:06:06] 
INFO [2025-10-14 16:06:06] $x
INFO [2025-10-14 16:06:06] $x$TF1
INFO [2025-10-14 16:06:06] [1] 4 5 6
INFO [2025-10-14 16:06:06] 
INFO [2025-10-14 16:06:06] $x$TF2
INFO [2025-10-14 16:06:06] [1] 1 2 3
INFO [2025-10-14 16:06:06] 
INFO [2025-10-14 16:06:06] 
INFO [2025-10-14 16:06:06] $disable.logging
INFO [2025-10-14 16:06:06] [1] TRUE
INFO [2025-10-14 16:06:06] 
INFO [2025-10-14 16:06:06] $filename
INFO [2025-10-14 16:06:06] NULL
INFO [2025-10-14 16:06:06] 
INFO [2025-10-14 16:06:07] $scaled
INFO [2025-10-14 16:06:07] [1] FALSE
INFO [2025-10-14 16:06:07] 
INFO [2025-10-14 16:06:07] $euler.d
INFO [2025-10-14 16:06:07] [1] FALSE
INFO [2025-10-14 16:06:07] 
INFO [2025-10-14 16:06:07] $cat.cex
INFO [2025-10-14 16:06:07] [1] 1
INFO [2025-10-14 16:06:07] 
INFO [2025-10-14 16:06:07] $cat.col
INFO [2025-10-14 16:06:07] [1] "black"
INFO [2025-10-14 16:06:07] 
INFO [2025-10-14 16:06:07] $cat.fontface
INFO [2025-10-14 16:06:07] [1] "plain"
INFO [2025-10-14 16:06:07] 
INFO [2025-10-14 16:06:07] $cat.fontfamily
INFO [2025-10-14 16:06:07] [1] "serif"
INFO [2025-10-14 16:06:07] 
INFO [2025-10-14 16:06:07] $x
INFO [2025-10-14 16:06:07] $x$TF1
INFO [2025-10-14 16:06:07] [1] 4 5 6
INFO [2025-10-14 16:06:07] 
INFO [2025-10-14 16:06:07] $x$TF2
INFO [2025-10-14 16:06:07] [1] 1 2 3
INFO [2025-10-14 16:06:07] 
INFO [2025-10-14 16:06:07] 
INFO [2025-10-14 16:06:07] $disable.logging
INFO [2025-10-14 16:06:07] [1] TRUE
INFO [2025-10-14 16:06:07] 
INFO [2025-10-14 16:06:07] $filename
INFO [2025-10-14 16:06:07] NULL
INFO [2025-10-14 16:06:07] 
INFO [2025-10-14 16:06:07] $scaled
INFO [2025-10-14 16:06:07] [1] FALSE
INFO [2025-10-14 16:06:07] 
INFO [2025-10-14 16:06:07] $euler.d
INFO [2025-10-14 16:06:07] [1] FALSE
INFO [2025-10-14 16:06:07] 
INFO [2025-10-14 16:06:07] $cat.cex
INFO [2025-10-14 16:06:07] [1] 1
INFO [2025-10-14 16:06:07] 
INFO [2025-10-14 16:06:07] $cat.col
INFO [2025-10-14 16:06:07] [1] "black"
INFO [2025-10-14 16:06:07] 
INFO [2025-10-14 16:06:07] $cat.fontface
INFO [2025-10-14 16:06:07] [1] "plain"
INFO [2025-10-14 16:06:07] 
INFO [2025-10-14 16:06:07] $cat.fontfamily
INFO [2025-10-14 16:06:07] [1] "serif"
INFO [2025-10-14 16:06:07] 
INFO [2025-10-14 16:06:07] $x
INFO [2025-10-14 16:06:07] $x$TF1
INFO [2025-10-14 16:06:07] [1] 4 5 6
INFO [2025-10-14 16:06:07] 
INFO [2025-10-14 16:06:07] $x$TF2
INFO [2025-10-14 16:06:07] [1] 1 2 3
INFO [2025-10-14 16:06:07] 
INFO [2025-10-14 16:06:07] $x$TF3
INFO [2025-10-14 16:06:07] [1] 2 3 6
INFO [2025-10-14 16:06:07] 
INFO [2025-10-14 16:06:07] 
INFO [2025-10-14 16:06:07] $disable.logging
INFO [2025-10-14 16:06:07] [1] TRUE
INFO [2025-10-14 16:06:07] 
INFO [2025-10-14 16:06:07] $filename
INFO [2025-10-14 16:06:07] NULL
INFO [2025-10-14 16:06:07] 
INFO [2025-10-14 16:06:07] $scaled
INFO [2025-10-14 16:06:07] [1] FALSE
INFO [2025-10-14 16:06:07] 
INFO [2025-10-14 16:06:07] $euler.d
INFO [2025-10-14 16:06:07] [1] FALSE
INFO [2025-10-14 16:06:07] 
INFO [2025-10-14 16:06:07] $cat.cex
INFO [2025-10-14 16:06:07] [1] 1
INFO [2025-10-14 16:06:07] 
INFO [2025-10-14 16:06:07] $cat.col
INFO [2025-10-14 16:06:07] [1] "black"
INFO [2025-10-14 16:06:07] 
INFO [2025-10-14 16:06:07] $cat.fontface
INFO [2025-10-14 16:06:07] [1] "plain"
INFO [2025-10-14 16:06:07] 
INFO [2025-10-14 16:06:07] $cat.fontfamily
INFO [2025-10-14 16:06:07] [1] "serif"
INFO [2025-10-14 16:06:07] 
INFO [2025-10-14 16:06:07] $x
INFO [2025-10-14 16:06:07] $x$TF1
INFO [2025-10-14 16:06:07] [1] 3 4 5
INFO [2025-10-14 16:06:07] 
INFO [2025-10-14 16:06:07] $x$TF2
INFO [2025-10-14 16:06:07] [1] 1 2 5
INFO [2025-10-14 16:06:07] 
INFO [2025-10-14 16:06:07] $x$TF3
INFO [2025-10-14 16:06:07] [1] 1 2 5
INFO [2025-10-14 16:06:07] 
INFO [2025-10-14 16:06:07] 
INFO [2025-10-14 16:06:07] $disable.logging
INFO [2025-10-14 16:06:07] [1] TRUE
INFO [2025-10-14 16:06:07] 
INFO [2025-10-14 16:06:07] $filename
INFO [2025-10-14 16:06:07] NULL
INFO [2025-10-14 16:06:07] 
INFO [2025-10-14 16:06:08] $scaled
INFO [2025-10-14 16:06:08] [1] FALSE
INFO [2025-10-14 16:06:08] 
INFO [2025-10-14 16:06:08] $euler.d
INFO [2025-10-14 16:06:08] [1] FALSE
INFO [2025-10-14 16:06:08] 
INFO [2025-10-14 16:06:08] $cat.cex
INFO [2025-10-14 16:06:08] [1] 1
INFO [2025-10-14 16:06:08] 
INFO [2025-10-14 16:06:08] $cat.col
INFO [2025-10-14 16:06:08] [1] "black"
INFO [2025-10-14 16:06:08] 
INFO [2025-10-14 16:06:08] $cat.fontface
INFO [2025-10-14 16:06:08] [1] "plain"
INFO [2025-10-14 16:06:08] 
INFO [2025-10-14 16:06:08] $cat.fontfamily
INFO [2025-10-14 16:06:08] [1] "serif"
INFO [2025-10-14 16:06:08] 
INFO [2025-10-14 16:06:08] $x
INFO [2025-10-14 16:06:08] $x$TF1
INFO [2025-10-14 16:06:08] [1] 3 4 5
INFO [2025-10-14 16:06:08] 
INFO [2025-10-14 16:06:08] $x$TF2
INFO [2025-10-14 16:06:08] [1] 1 2 5
INFO [2025-10-14 16:06:08] 
INFO [2025-10-14 16:06:08] $x$TF3
INFO [2025-10-14 16:06:08] [1] 1 2 5
INFO [2025-10-14 16:06:08] 
INFO [2025-10-14 16:06:08] $x$TF4
INFO [2025-10-14 16:06:08] [1] 1 2 5
INFO [2025-10-14 16:06:08] 
INFO [2025-10-14 16:06:08] 
INFO [2025-10-14 16:06:08] $disable.logging
INFO [2025-10-14 16:06:08] [1] TRUE
INFO [2025-10-14 16:06:08] 
INFO [2025-10-14 16:06:08] $filename
INFO [2025-10-14 16:06:08] NULL
INFO [2025-10-14 16:06:08] 
[ 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 
183.501   5.212 196.884 

Example timings

ChIPpeakAnno.Rcheck/ChIPpeakAnno-Ex.timings

nameusersystemelapsed
ChIPpeakAnno-package0.0000.0000.001
ExonPlusUtr.human.GRCh375.0080.1505.241
HOT.spots0.1890.0120.203
IDRfilter0.0010.0010.001
Peaks.Ste12.Replicate10.0510.0040.055
Peaks.Ste12.Replicate20.0130.0030.016
Peaks.Ste12.Replicate30.0120.0030.015
TSS.human.GRCh370.1730.0100.185
TSS.human.GRCh380.3330.0170.355
TSS.human.NCBI360.1770.0100.187
TSS.mouse.GRCm380.1690.0120.183
TSS.mouse.NCBIM370.1420.0060.150
TSS.rat.RGSC3.40.1280.0060.138
TSS.rat.Rnor_5.00.1060.0060.112
TSS.zebrafish.Zv80.1170.0080.124
TSS.zebrafish.Zv90.1400.0070.151
addAncestors1.3110.0571.376
addGeneIDs2.8170.6633.547
addMetadata1.2180.0901.318
annoGR0.0000.0010.000
annoPeaks3.4980.2945.990
annotatePeakInBatch14.087 0.63014.939
annotatedPeak0.0870.0040.092
assignChromosomeRegion0.0020.0010.002
bdp0.0010.0000.000
binOverFeature0.8760.0260.911
binOverGene0.0010.0000.001
binOverRegions0.0010.0010.001
condenseMatrixByColnames0.0110.0010.011
convert2EntrezID0.5320.0060.542
countPatternInSeqs0.1830.0050.191
cumulativePercentage0.0000.0000.001
downstreams0.0240.0000.026
egOrgMap0.0010.0000.000
enrichedGO0.0030.0020.005
enrichmentPlot0.7040.0110.717
estFragmentLength0.0010.0000.001
estLibSize0.0010.0000.000
featureAlignedDistribution0.3280.0050.339
featureAlignedExtendSignal0.0020.0000.003
featureAlignedHeatmap0.3280.0030.335
featureAlignedSignal0.1830.0420.228
findEnhancers24.407 0.58625.353
findMotifsInPromoterSeqs17.325 0.54218.291
findOverlappingPeaks0.0010.0000.002
findOverlapsOfPeaks1.8620.0271.921
genomicElementDistribution0.0020.0000.003
genomicElementUpSetR0.0010.0000.001
getAllPeakSequence0.6100.0340.671
getAnnotation0.0010.0010.003
getEnrichedGO0.0120.0060.019
getEnrichedPATH0.0010.0000.002
getGO0.0010.0010.000
getGeneSeq0.0020.0010.002
getUniqueGOidCount0.0010.0000.001
getVennCounts0.0020.0010.001
hyperGtest0.0010.0010.001
makeVennDiagram0.0040.0000.004
mergePlusMinusPeaks0.0010.0000.001
metagenePlot2.4600.0802.557
myPeakList0.0270.0030.029
oligoFrequency0.1190.0070.127
oligoSummary0.0010.0000.001
peakPermTest0.0020.0010.003
peaks10.0080.0020.010
peaks20.0080.0030.011
peaks30.0070.0020.010
peaksNearBDP0.0010.0000.001
pie10.0050.0020.006
plotBinOverRegions0.0010.0010.001
preparePool0.0000.0000.001
reCenterPeaks0.0250.0010.027
summarizeOverlapsByBins7.2000.5077.475
summarizePatternInPeaks1.4450.4081.872
tileCount0.3730.4100.484
tileGRanges0.0380.0230.060
toGRanges0.0860.0360.123
translatePattern0.0000.0010.001
wgEncodeTfbsV30.3100.0170.328
write2FASTA0.0140.0050.020
xget0.1250.0170.142