Multiple platform build/check report for BioC 3.22 - CHECK results for ChIPpeakAnno on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"	4901
lconway	macOS 12.7.6 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4691
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4637
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*

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: 3.43.2

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_3.43.2.tar.gz

StartedAt: 2025-10-28 20:06:28 -0400 (Tue, 28 Oct 2025)

EndedAt: 2025-10-28 20:18:24 -0400 (Tue, 28 Oct 2025)

EllapsedTime: 716.0 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_3.43.2.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 ‘3.43.2’
* 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            28.933  0.930  30.005
findMotifsInPromoterSeqs 17.737  0.461  18.511
annotatePeakInBatch      15.378  0.732  16.223
summarizeOverlapsByBins   6.019  0.530   6.212
* 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 ‘3.43.2’
** 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 [2025-10-28 20:17:56] $cat.cex
INFO [2025-10-28 20:17:56] [1] 1
INFO [2025-10-28 20:17:56] 
INFO [2025-10-28 20:17:56] $cat.col
INFO [2025-10-28 20:17:56] [1] "black"
INFO [2025-10-28 20:17:56] 
INFO [2025-10-28 20:17:56] $cat.fontface
INFO [2025-10-28 20:17:56] [1] "plain"
INFO [2025-10-28 20:17:56] 
INFO [2025-10-28 20:17:56] $cat.fontfamily
INFO [2025-10-28 20:17:56] [1] "serif"
INFO [2025-10-28 20:17:56] 
INFO [2025-10-28 20:17:56] $x
INFO [2025-10-28 20:17:56] $x$TF1
INFO [2025-10-28 20:17:56] [1] 3 4 5
INFO [2025-10-28 20:17:56] 
INFO [2025-10-28 20:17:56] $x$TF2
INFO [2025-10-28 20:17:56] [1] 1 2 3 4 5
INFO [2025-10-28 20:17:56] 
INFO [2025-10-28 20:17:56] 
INFO [2025-10-28 20:17:56] $disable.logging
INFO [2025-10-28 20:17:56] [1] TRUE
INFO [2025-10-28 20:17:56] 
INFO [2025-10-28 20:17:56] $filename
INFO [2025-10-28 20:17:56] NULL
INFO [2025-10-28 20:17:56] 
INFO [2025-10-28 20:17:56] $cat.cex
INFO [2025-10-28 20:17:56] [1] 1
INFO [2025-10-28 20:17:56] 
INFO [2025-10-28 20:17:56] $cat.col
INFO [2025-10-28 20:17:56] [1] "black"
INFO [2025-10-28 20:17:56] 
INFO [2025-10-28 20:17:56] $cat.fontface
INFO [2025-10-28 20:17:56] [1] "plain"
INFO [2025-10-28 20:17:56] 
INFO [2025-10-28 20:17:56] $cat.fontfamily
INFO [2025-10-28 20:17:56] [1] "serif"
INFO [2025-10-28 20:17:56] 
INFO [2025-10-28 20:17:56] $x
INFO [2025-10-28 20:17:56] $x$TF1
INFO [2025-10-28 20:17:56] [1] 3 4 5
INFO [2025-10-28 20:17:56] 
INFO [2025-10-28 20:17:56] $x$TF2
INFO [2025-10-28 20:17:56] [1] 1 2 4 5
INFO [2025-10-28 20:17:56] 
INFO [2025-10-28 20:17:56] $x$TF3
INFO [2025-10-28 20:17:56] [1] 3 4 5
INFO [2025-10-28 20:17:56] 
INFO [2025-10-28 20:17:56] $x$TF4
INFO [2025-10-28 20:17:56] [1] 1 2 4 5
INFO [2025-10-28 20:17:56] 
INFO [2025-10-28 20:17:56] 
INFO [2025-10-28 20:17:56] $disable.logging
INFO [2025-10-28 20:17:56] [1] TRUE
INFO [2025-10-28 20:17:56] 
INFO [2025-10-28 20:17:56] $filename
INFO [2025-10-28 20:17:56] NULL
INFO [2025-10-28 20:17:56] 
INFO [2025-10-28 20:17:57] $scaled
INFO [2025-10-28 20:17:57] [1] FALSE
INFO [2025-10-28 20:17:57] 
INFO [2025-10-28 20:17:57] $euler.d
INFO [2025-10-28 20:17:57] [1] FALSE
INFO [2025-10-28 20:17:57] 
INFO [2025-10-28 20:17:57] $cat.cex
INFO [2025-10-28 20:17:57] [1] 1
INFO [2025-10-28 20:17:57] 
INFO [2025-10-28 20:17:57] $cat.col
INFO [2025-10-28 20:17:57] [1] "black"
INFO [2025-10-28 20:17:57] 
INFO [2025-10-28 20:17:57] $cat.fontface
INFO [2025-10-28 20:17:57] [1] "plain"
INFO [2025-10-28 20:17:57] 
INFO [2025-10-28 20:17:57] $cat.fontfamily
INFO [2025-10-28 20:17:57] [1] "serif"
INFO [2025-10-28 20:17:57] 
INFO [2025-10-28 20:17:57] $x
INFO [2025-10-28 20:17:57] $x$TF1
INFO [2025-10-28 20:17:57] [1] 1 2 3
INFO [2025-10-28 20:17:57] 
INFO [2025-10-28 20:17:57] $x$TF2
INFO [2025-10-28 20:17:57] [1] 1 2 3
INFO [2025-10-28 20:17:57] 
INFO [2025-10-28 20:17:57] 
INFO [2025-10-28 20:17:57] $disable.logging
INFO [2025-10-28 20:17:57] [1] TRUE
INFO [2025-10-28 20:17:57] 
INFO [2025-10-28 20:17:57] $filename
INFO [2025-10-28 20:17:57] NULL
INFO [2025-10-28 20:17:57] 
INFO [2025-10-28 20:17:57] $scaled
INFO [2025-10-28 20:17:57] [1] FALSE
INFO [2025-10-28 20:17:57] 
INFO [2025-10-28 20:17:57] $euler.d
INFO [2025-10-28 20:17:57] [1] FALSE
INFO [2025-10-28 20:17:57] 
INFO [2025-10-28 20:17:57] $cat.cex
INFO [2025-10-28 20:17:57] [1] 1
INFO [2025-10-28 20:17:57] 
INFO [2025-10-28 20:17:57] $cat.col
INFO [2025-10-28 20:17:57] [1] "black"
INFO [2025-10-28 20:17:57] 
INFO [2025-10-28 20:17:57] $cat.fontface
INFO [2025-10-28 20:17:57] [1] "plain"
INFO [2025-10-28 20:17:57] 
INFO [2025-10-28 20:17:57] $cat.fontfamily
INFO [2025-10-28 20:17:57] [1] "serif"
INFO [2025-10-28 20:17:57] 
INFO [2025-10-28 20:17:57] $x
INFO [2025-10-28 20:17:57] $x$TF1
INFO [2025-10-28 20:17:57] [1] 4 5 6
INFO [2025-10-28 20:17:57] 
INFO [2025-10-28 20:17:57] $x$TF2
INFO [2025-10-28 20:17:57] [1] 1 2 3
INFO [2025-10-28 20:17:57] 
INFO [2025-10-28 20:17:57] 
INFO [2025-10-28 20:17:57] $disable.logging
INFO [2025-10-28 20:17:57] [1] TRUE
INFO [2025-10-28 20:17:57] 
INFO [2025-10-28 20:17:57] $filename
INFO [2025-10-28 20:17:57] NULL
INFO [2025-10-28 20:17:57] 
INFO [2025-10-28 20:17:57] $scaled
INFO [2025-10-28 20:17:57] [1] FALSE
INFO [2025-10-28 20:17:57] 
INFO [2025-10-28 20:17:57] $euler.d
INFO [2025-10-28 20:17:57] [1] FALSE
INFO [2025-10-28 20:17:57] 
INFO [2025-10-28 20:17:57] $cat.cex
INFO [2025-10-28 20:17:57] [1] 1
INFO [2025-10-28 20:17:57] 
INFO [2025-10-28 20:17:57] $cat.col
INFO [2025-10-28 20:17:57] [1] "black"
INFO [2025-10-28 20:17:57] 
INFO [2025-10-28 20:17:57] $cat.fontface
INFO [2025-10-28 20:17:57] [1] "plain"
INFO [2025-10-28 20:17:57] 
INFO [2025-10-28 20:17:57] $cat.fontfamily
INFO [2025-10-28 20:17:57] [1] "serif"
INFO [2025-10-28 20:17:57] 
INFO [2025-10-28 20:17:57] $x
INFO [2025-10-28 20:17:57] $x$TF1
INFO [2025-10-28 20:17:57] [1] 4 5 6
INFO [2025-10-28 20:17:57] 
INFO [2025-10-28 20:17:57] $x$TF2
INFO [2025-10-28 20:17:57] [1] 1 2 3
INFO [2025-10-28 20:17:57] 
INFO [2025-10-28 20:17:57] 
INFO [2025-10-28 20:17:57] $disable.logging
INFO [2025-10-28 20:17:57] [1] TRUE
INFO [2025-10-28 20:17:57] 
INFO [2025-10-28 20:17:57] $filename
INFO [2025-10-28 20:17:57] NULL
INFO [2025-10-28 20:17:57] 
INFO [2025-10-28 20:17:57] $scaled
INFO [2025-10-28 20:17:57] [1] FALSE
INFO [2025-10-28 20:17:57] 
INFO [2025-10-28 20:17:57] $euler.d
INFO [2025-10-28 20:17:57] [1] FALSE
INFO [2025-10-28 20:17:57] 
INFO [2025-10-28 20:17:57] $cat.cex
INFO [2025-10-28 20:17:57] [1] 1
INFO [2025-10-28 20:17:57] 
INFO [2025-10-28 20:17:57] $cat.col
INFO [2025-10-28 20:17:57] [1] "black"
INFO [2025-10-28 20:17:57] 
INFO [2025-10-28 20:17:57] $cat.fontface
INFO [2025-10-28 20:17:57] [1] "plain"
INFO [2025-10-28 20:17:57] 
INFO [2025-10-28 20:17:57] $cat.fontfamily
INFO [2025-10-28 20:17:57] [1] "serif"
INFO [2025-10-28 20:17:57] 
INFO [2025-10-28 20:17:57] $x
INFO [2025-10-28 20:17:57] $x$TF1
INFO [2025-10-28 20:17:57] [1] 4 5 6
INFO [2025-10-28 20:17:57] 
INFO [2025-10-28 20:17:57] $x$TF2
INFO [2025-10-28 20:17:57] [1] 1 2 3
INFO [2025-10-28 20:17:57] 
INFO [2025-10-28 20:17:57] $x$TF3
INFO [2025-10-28 20:17:57] [1] 2 3 6
INFO [2025-10-28 20:17:57] 
INFO [2025-10-28 20:17:57] 
INFO [2025-10-28 20:17:57] $disable.logging
INFO [2025-10-28 20:17:57] [1] TRUE
INFO [2025-10-28 20:17:57] 
INFO [2025-10-28 20:17:57] $filename
INFO [2025-10-28 20:17:57] NULL
INFO [2025-10-28 20:17:57] 
INFO [2025-10-28 20:17:58] $scaled
INFO [2025-10-28 20:17:58] [1] FALSE
INFO [2025-10-28 20:17:58] 
INFO [2025-10-28 20:17:58] $euler.d
INFO [2025-10-28 20:17:58] [1] FALSE
INFO [2025-10-28 20:17:58] 
INFO [2025-10-28 20:17:58] $cat.cex
INFO [2025-10-28 20:17:58] [1] 1
INFO [2025-10-28 20:17:58] 
INFO [2025-10-28 20:17:58] $cat.col
INFO [2025-10-28 20:17:58] [1] "black"
INFO [2025-10-28 20:17:58] 
INFO [2025-10-28 20:17:58] $cat.fontface
INFO [2025-10-28 20:17:58] [1] "plain"
INFO [2025-10-28 20:17:58] 
INFO [2025-10-28 20:17:58] $cat.fontfamily
INFO [2025-10-28 20:17:58] [1] "serif"
INFO [2025-10-28 20:17:58] 
INFO [2025-10-28 20:17:58] $x
INFO [2025-10-28 20:17:58] $x$TF1
INFO [2025-10-28 20:17:58] [1] 3 4 5
INFO [2025-10-28 20:17:58] 
INFO [2025-10-28 20:17:58] $x$TF2
INFO [2025-10-28 20:17:58] [1] 1 2 5
INFO [2025-10-28 20:17:58] 
INFO [2025-10-28 20:17:58] $x$TF3
INFO [2025-10-28 20:17:58] [1] 1 2 5
INFO [2025-10-28 20:17:58] 
INFO [2025-10-28 20:17:58] 
INFO [2025-10-28 20:17:58] $disable.logging
INFO [2025-10-28 20:17:58] [1] TRUE
INFO [2025-10-28 20:17:58] 
INFO [2025-10-28 20:17:58] $filename
INFO [2025-10-28 20:17:58] NULL
INFO [2025-10-28 20:17:58] 
INFO [2025-10-28 20:17:58] $scaled
INFO [2025-10-28 20:17:58] [1] FALSE
INFO [2025-10-28 20:17:58] 
INFO [2025-10-28 20:17:58] $euler.d
INFO [2025-10-28 20:17:58] [1] FALSE
INFO [2025-10-28 20:17:58] 
INFO [2025-10-28 20:17:58] $cat.cex
INFO [2025-10-28 20:17:58] [1] 1
INFO [2025-10-28 20:17:58] 
INFO [2025-10-28 20:17:58] $cat.col
INFO [2025-10-28 20:17:58] [1] "black"
INFO [2025-10-28 20:17:58] 
INFO [2025-10-28 20:17:58] $cat.fontface
INFO [2025-10-28 20:17:58] [1] "plain"
INFO [2025-10-28 20:17:58] 
INFO [2025-10-28 20:17:58] $cat.fontfamily
INFO [2025-10-28 20:17:58] [1] "serif"
INFO [2025-10-28 20:17:58] 
INFO [2025-10-28 20:17:58] $x
INFO [2025-10-28 20:17:58] $x$TF1
INFO [2025-10-28 20:17:58] [1] 3 4 5
INFO [2025-10-28 20:17:58] 
INFO [2025-10-28 20:17:58] $x$TF2
INFO [2025-10-28 20:17:58] [1] 1 2 5
INFO [2025-10-28 20:17:58] 
INFO [2025-10-28 20:17:58] $x$TF3
INFO [2025-10-28 20:17:58] [1] 1 2 5
INFO [2025-10-28 20:17:58] 
INFO [2025-10-28 20:17:58] $x$TF4
INFO [2025-10-28 20:17:58] [1] 1 2 5
INFO [2025-10-28 20:17:58] 
INFO [2025-10-28 20:17:58] 
INFO [2025-10-28 20:17:58] $disable.logging
INFO [2025-10-28 20:17:58] [1] TRUE
INFO [2025-10-28 20:17:58] 
INFO [2025-10-28 20:17:58] $filename
INFO [2025-10-28 20:17:58] NULL
INFO [2025-10-28 20:17:58] 
[ 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 
213.953   6.851 223.450

Example timings

ChIPpeakAnno.Rcheck/ChIPpeakAnno-Ex.timings

name	user	system	elapsed
ChIPpeakAnno-package	0.001	0.001	0.002
ExonPlusUtr.human.GRCh37	3.408	0.103	3.538
HOT.spots	0.098	0.009	0.107
IDRfilter	0.001	0.001	0.001
Peaks.Ste12.Replicate1	0.055	0.003	0.057
Peaks.Ste12.Replicate2	0.012	0.002	0.014
Peaks.Ste12.Replicate3	0.014	0.002	0.016
TSS.human.GRCh37	0.094	0.005	0.101
TSS.human.GRCh38	0.204	0.014	0.219
TSS.human.NCBI36	0.087	0.006	0.095
TSS.mouse.GRCm38	0.079	0.005	0.085
TSS.mouse.NCBIM37	0.073	0.006	0.080
TSS.rat.RGSC3.4	0.059	0.004	0.062
TSS.rat.Rnor_5.0	0.057	0.003	0.061
TSS.zebrafish.Zv8	0.061	0.005	0.067
TSS.zebrafish.Zv9	0.068	0.004	0.073
addAncestors	1.200	0.093	1.331
addGeneIDs	2.627	1.037	3.721
addMetadata	1.237	0.097	1.343
annoGR	0.000	0.000	0.001
annoPeaks	3.372	0.320	3.763
annotatePeakInBatch	15.378	0.732	16.223
annotatedPeak	0.054	0.004	0.058
assignChromosomeRegion	0.001	0.001	0.002
bdp	0.000	0.000	0.001
binOverFeature	0.784	0.020	0.807
binOverGene	0.001	0.000	0.001
binOverRegions	0.001	0.000	0.002
condenseMatrixByColnames	0.012	0.000	0.012
convert2EntrezID	0.504	0.007	0.513
countPatternInSeqs	0.178	0.006	0.184
cumulativePercentage	0	0	0
downstreams	0.026	0.000	0.026
egOrgMap	0	0	0
enrichedGO	0.002	0.002	0.004
enrichmentPlot	0.883	0.023	0.911
estFragmentLength	0	0	0
estLibSize	0	0	0
featureAlignedDistribution	0.248	0.002	0.251
featureAlignedExtendSignal	0.002	0.000	0.002
featureAlignedHeatmap	0.357	0.003	0.362
featureAlignedSignal	0.215	0.048	0.265
findEnhancers	28.933	0.930	30.005
findMotifsInPromoterSeqs	17.737	0.461	18.511
findOverlappingPeaks	0.001	0.000	0.002
findOverlapsOfPeaks	2.222	0.038	2.277
genomicElementDistribution	0.002	0.001	0.003
genomicElementUpSetR	0.001	0.000	0.002
getAllPeakSequence	0.626	0.025	0.660
getAnnotation	0.001	0.001	0.001
getEnrichedGO	0.011	0.004	0.015
getEnrichedPATH	0.001	0.000	0.001
getGO	0.001	0.000	0.001
getGeneSeq	0.002	0.000	0.002
getUniqueGOidCount	0.001	0.000	0.002
getVennCounts	0.001	0.001	0.002
hyperGtest	0.001	0.001	0.002
makeVennDiagram	0.004	0.001	0.004
mergePlusMinusPeaks	0	0	0
metagenePlot	4.006	0.112	4.142
myPeakList	0.015	0.002	0.017
oligoFrequency	0.112	0.009	0.122
oligoSummary	0.000	0.000	0.001
peakPermTest	0.002	0.001	0.003
peaks1	0.136	0.027	0.164
peaks2	0.009	0.002	0.010
peaks3	0.006	0.002	0.008
peaksNearBDP	0.001	0.000	0.000
pie1	0.004	0.002	0.006
plotBinOverRegions	0.000	0.000	0.001
preparePool	0.001	0.001	0.001
reCenterPeaks	0.025	0.001	0.025
summarizeOverlapsByBins	6.019	0.530	6.212
summarizePatternInPeaks	1.815	0.254	2.084
tileCount	0.445	0.401	0.521
tileGRanges	0.043	0.011	0.055
toGRanges	0.100	0.014	0.118
translatePattern	0.000	0.001	0.000
wgEncodeTfbsV3	0.149	0.015	0.164
write2FASTA	0.021	0.003	0.025
xget	0.154	0.013	0.167