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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 337/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPpeakAnno 3.40.0  (landing page)
Jianhong Ou
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/ChIPpeakAnno
git_branch: RELEASE_3_20
git_last_commit: faf2e4f
git_last_commit_date: 2024-10-29 09:32:01 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for ChIPpeakAnno on merida1

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: 3.40.0
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_3.40.0.tar.gz
StartedAt: 2024-12-20 01:04:02 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 01:27:26 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 1403.5 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_3.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ChIPpeakAnno.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* 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 ‘3.40.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ... NOTE
  installed size is 21.1Mb
  sub-directories of 1Mb or more:
    R         1.1Mb
    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            61.331  1.119  65.599
findMotifsInPromoterSeqs 34.279  0.518  36.775
annotatePeakInBatch      28.197  1.137  31.140
summarizeOverlapsByBins   7.271  0.751   7.819
annoPeaks                 6.091  0.632   7.653
addGeneIDs                4.043  1.223   5.525
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/ChIPpeakAnno.Rcheck/00check.log’
for details.


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/4.4-x86_64/Resources/library’
* installing *source* package ‘ChIPpeakAnno’ ...
** 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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 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

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
    tapply, union, 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

Attaching package: 'rtracklayer'

The following object is masked from 'package:BiocIO':

    FileForFormat

[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 [2024-12-20 01:26:26] $cat.cex
INFO [2024-12-20 01:26:26] [1] 1
INFO [2024-12-20 01:26:26] 
INFO [2024-12-20 01:26:26] $cat.col
INFO [2024-12-20 01:26:26] [1] "black"
INFO [2024-12-20 01:26:26] 
INFO [2024-12-20 01:26:26] $cat.fontface
INFO [2024-12-20 01:26:26] [1] "plain"
INFO [2024-12-20 01:26:26] 
INFO [2024-12-20 01:26:26] $cat.fontfamily
INFO [2024-12-20 01:26:26] [1] "serif"
INFO [2024-12-20 01:26:26] 
INFO [2024-12-20 01:26:26] $x
INFO [2024-12-20 01:26:26] $x$TF1
INFO [2024-12-20 01:26:26] [1] 3 4 5
INFO [2024-12-20 01:26:26] 
INFO [2024-12-20 01:26:26] $x$TF2
INFO [2024-12-20 01:26:26] [1] 1 2 3 4 5
INFO [2024-12-20 01:26:26] 
INFO [2024-12-20 01:26:26] 
INFO [2024-12-20 01:26:26] $disable.logging
INFO [2024-12-20 01:26:26] [1] TRUE
INFO [2024-12-20 01:26:26] 
INFO [2024-12-20 01:26:26] $filename
INFO [2024-12-20 01:26:26] NULL
INFO [2024-12-20 01:26:26] 
INFO [2024-12-20 01:26:27] $cat.cex
INFO [2024-12-20 01:26:27] [1] 1
INFO [2024-12-20 01:26:27] 
INFO [2024-12-20 01:26:27] $cat.col
INFO [2024-12-20 01:26:27] [1] "black"
INFO [2024-12-20 01:26:27] 
INFO [2024-12-20 01:26:27] $cat.fontface
INFO [2024-12-20 01:26:27] [1] "plain"
INFO [2024-12-20 01:26:27] 
INFO [2024-12-20 01:26:27] $cat.fontfamily
INFO [2024-12-20 01:26:27] [1] "serif"
INFO [2024-12-20 01:26:27] 
INFO [2024-12-20 01:26:27] $x
INFO [2024-12-20 01:26:27] $x$TF1
INFO [2024-12-20 01:26:27] [1] 3 4 5
INFO [2024-12-20 01:26:27] 
INFO [2024-12-20 01:26:27] $x$TF2
INFO [2024-12-20 01:26:27] [1] 1 2 4 5
INFO [2024-12-20 01:26:27] 
INFO [2024-12-20 01:26:27] $x$TF3
INFO [2024-12-20 01:26:27] [1] 3 4 5
INFO [2024-12-20 01:26:27] 
INFO [2024-12-20 01:26:27] $x$TF4
INFO [2024-12-20 01:26:27] [1] 1 2 4 5
INFO [2024-12-20 01:26:27] 
INFO [2024-12-20 01:26:27] 
INFO [2024-12-20 01:26:27] $disable.logging
INFO [2024-12-20 01:26:27] [1] TRUE
INFO [2024-12-20 01:26:27] 
INFO [2024-12-20 01:26:27] $filename
INFO [2024-12-20 01:26:27] NULL
INFO [2024-12-20 01:26:27] 
INFO [2024-12-20 01:26:28] $scaled
INFO [2024-12-20 01:26:28] [1] FALSE
INFO [2024-12-20 01:26:28] 
INFO [2024-12-20 01:26:28] $euler.d
INFO [2024-12-20 01:26:28] [1] FALSE
INFO [2024-12-20 01:26:28] 
INFO [2024-12-20 01:26:28] $cat.cex
INFO [2024-12-20 01:26:28] [1] 1
INFO [2024-12-20 01:26:28] 
INFO [2024-12-20 01:26:28] $cat.col
INFO [2024-12-20 01:26:28] [1] "black"
INFO [2024-12-20 01:26:28] 
INFO [2024-12-20 01:26:28] $cat.fontface
INFO [2024-12-20 01:26:28] [1] "plain"
INFO [2024-12-20 01:26:28] 
INFO [2024-12-20 01:26:28] $cat.fontfamily
INFO [2024-12-20 01:26:28] [1] "serif"
INFO [2024-12-20 01:26:28] 
INFO [2024-12-20 01:26:28] $x
INFO [2024-12-20 01:26:28] $x$TF1
INFO [2024-12-20 01:26:28] [1] 1 2 3
INFO [2024-12-20 01:26:28] 
INFO [2024-12-20 01:26:28] $x$TF2
INFO [2024-12-20 01:26:28] [1] 1 2 3
INFO [2024-12-20 01:26:28] 
INFO [2024-12-20 01:26:28] 
INFO [2024-12-20 01:26:28] $disable.logging
INFO [2024-12-20 01:26:28] [1] TRUE
INFO [2024-12-20 01:26:28] 
INFO [2024-12-20 01:26:28] $filename
INFO [2024-12-20 01:26:28] NULL
INFO [2024-12-20 01:26:28] 
INFO [2024-12-20 01:26:29] $scaled
INFO [2024-12-20 01:26:29] [1] FALSE
INFO [2024-12-20 01:26:29] 
INFO [2024-12-20 01:26:29] $euler.d
INFO [2024-12-20 01:26:29] [1] FALSE
INFO [2024-12-20 01:26:29] 
INFO [2024-12-20 01:26:29] $cat.cex
INFO [2024-12-20 01:26:29] [1] 1
INFO [2024-12-20 01:26:29] 
INFO [2024-12-20 01:26:29] $cat.col
INFO [2024-12-20 01:26:29] [1] "black"
INFO [2024-12-20 01:26:29] 
INFO [2024-12-20 01:26:29] $cat.fontface
INFO [2024-12-20 01:26:29] [1] "plain"
INFO [2024-12-20 01:26:29] 
INFO [2024-12-20 01:26:29] $cat.fontfamily
INFO [2024-12-20 01:26:29] [1] "serif"
INFO [2024-12-20 01:26:29] 
INFO [2024-12-20 01:26:29] $x
INFO [2024-12-20 01:26:29] $x$TF1
INFO [2024-12-20 01:26:29] [1] 4 5 6
INFO [2024-12-20 01:26:29] 
INFO [2024-12-20 01:26:29] $x$TF2
INFO [2024-12-20 01:26:29] [1] 1 2 3
INFO [2024-12-20 01:26:29] 
INFO [2024-12-20 01:26:29] 
INFO [2024-12-20 01:26:29] $disable.logging
INFO [2024-12-20 01:26:29] [1] TRUE
INFO [2024-12-20 01:26:29] 
INFO [2024-12-20 01:26:29] $filename
INFO [2024-12-20 01:26:29] NULL
INFO [2024-12-20 01:26:29] 
INFO [2024-12-20 01:26:30] $scaled
INFO [2024-12-20 01:26:30] [1] FALSE
INFO [2024-12-20 01:26:30] 
INFO [2024-12-20 01:26:30] $euler.d
INFO [2024-12-20 01:26:30] [1] FALSE
INFO [2024-12-20 01:26:30] 
INFO [2024-12-20 01:26:30] $cat.cex
INFO [2024-12-20 01:26:30] [1] 1
INFO [2024-12-20 01:26:30] 
INFO [2024-12-20 01:26:30] $cat.col
INFO [2024-12-20 01:26:30] [1] "black"
INFO [2024-12-20 01:26:30] 
INFO [2024-12-20 01:26:30] $cat.fontface
INFO [2024-12-20 01:26:30] [1] "plain"
INFO [2024-12-20 01:26:30] 
INFO [2024-12-20 01:26:30] $cat.fontfamily
INFO [2024-12-20 01:26:30] [1] "serif"
INFO [2024-12-20 01:26:30] 
INFO [2024-12-20 01:26:30] $x
INFO [2024-12-20 01:26:30] $x$TF1
INFO [2024-12-20 01:26:30] [1] 4 5 6
INFO [2024-12-20 01:26:30] 
INFO [2024-12-20 01:26:30] $x$TF2
INFO [2024-12-20 01:26:30] [1] 1 2 3
INFO [2024-12-20 01:26:30] 
INFO [2024-12-20 01:26:30] 
INFO [2024-12-20 01:26:30] $disable.logging
INFO [2024-12-20 01:26:30] [1] TRUE
INFO [2024-12-20 01:26:30] 
INFO [2024-12-20 01:26:30] $filename
INFO [2024-12-20 01:26:30] NULL
INFO [2024-12-20 01:26:30] 
INFO [2024-12-20 01:26:30] $scaled
INFO [2024-12-20 01:26:30] [1] FALSE
INFO [2024-12-20 01:26:30] 
INFO [2024-12-20 01:26:30] $euler.d
INFO [2024-12-20 01:26:30] [1] FALSE
INFO [2024-12-20 01:26:30] 
INFO [2024-12-20 01:26:30] $cat.cex
INFO [2024-12-20 01:26:30] [1] 1
INFO [2024-12-20 01:26:30] 
INFO [2024-12-20 01:26:30] $cat.col
INFO [2024-12-20 01:26:30] [1] "black"
INFO [2024-12-20 01:26:30] 
INFO [2024-12-20 01:26:30] $cat.fontface
INFO [2024-12-20 01:26:30] [1] "plain"
INFO [2024-12-20 01:26:30] 
INFO [2024-12-20 01:26:30] $cat.fontfamily
INFO [2024-12-20 01:26:30] [1] "serif"
INFO [2024-12-20 01:26:30] 
INFO [2024-12-20 01:26:30] $x
INFO [2024-12-20 01:26:30] $x$TF1
INFO [2024-12-20 01:26:30] [1] 4 5 6
INFO [2024-12-20 01:26:30] 
INFO [2024-12-20 01:26:30] $x$TF2
INFO [2024-12-20 01:26:30] [1] 1 2 3
INFO [2024-12-20 01:26:30] 
INFO [2024-12-20 01:26:30] $x$TF3
INFO [2024-12-20 01:26:30] [1] 2 3 6
INFO [2024-12-20 01:26:30] 
INFO [2024-12-20 01:26:30] 
INFO [2024-12-20 01:26:30] $disable.logging
INFO [2024-12-20 01:26:30] [1] TRUE
INFO [2024-12-20 01:26:30] 
INFO [2024-12-20 01:26:30] $filename
INFO [2024-12-20 01:26:30] NULL
INFO [2024-12-20 01:26:30] 
INFO [2024-12-20 01:26:31] $scaled
INFO [2024-12-20 01:26:31] [1] FALSE
INFO [2024-12-20 01:26:31] 
INFO [2024-12-20 01:26:31] $euler.d
INFO [2024-12-20 01:26:31] [1] FALSE
INFO [2024-12-20 01:26:31] 
INFO [2024-12-20 01:26:31] $cat.cex
INFO [2024-12-20 01:26:31] [1] 1
INFO [2024-12-20 01:26:31] 
INFO [2024-12-20 01:26:31] $cat.col
INFO [2024-12-20 01:26:31] [1] "black"
INFO [2024-12-20 01:26:31] 
INFO [2024-12-20 01:26:31] $cat.fontface
INFO [2024-12-20 01:26:31] [1] "plain"
INFO [2024-12-20 01:26:31] 
INFO [2024-12-20 01:26:31] $cat.fontfamily
INFO [2024-12-20 01:26:31] [1] "serif"
INFO [2024-12-20 01:26:31] 
INFO [2024-12-20 01:26:31] $x
INFO [2024-12-20 01:26:31] $x$TF1
INFO [2024-12-20 01:26:31] [1] 3 4 5
INFO [2024-12-20 01:26:31] 
INFO [2024-12-20 01:26:31] $x$TF2
INFO [2024-12-20 01:26:31] [1] 1 2 5
INFO [2024-12-20 01:26:31] 
INFO [2024-12-20 01:26:31] $x$TF3
INFO [2024-12-20 01:26:31] [1] 1 2 5
INFO [2024-12-20 01:26:31] 
INFO [2024-12-20 01:26:31] 
INFO [2024-12-20 01:26:31] $disable.logging
INFO [2024-12-20 01:26:31] [1] TRUE
INFO [2024-12-20 01:26:31] 
INFO [2024-12-20 01:26:31] $filename
INFO [2024-12-20 01:26:31] NULL
INFO [2024-12-20 01:26:31] 
INFO [2024-12-20 01:26:32] $scaled
INFO [2024-12-20 01:26:32] [1] FALSE
INFO [2024-12-20 01:26:32] 
INFO [2024-12-20 01:26:32] $euler.d
INFO [2024-12-20 01:26:32] [1] FALSE
INFO [2024-12-20 01:26:32] 
INFO [2024-12-20 01:26:32] $cat.cex
INFO [2024-12-20 01:26:32] [1] 1
INFO [2024-12-20 01:26:32] 
INFO [2024-12-20 01:26:32] $cat.col
INFO [2024-12-20 01:26:32] [1] "black"
INFO [2024-12-20 01:26:32] 
INFO [2024-12-20 01:26:32] $cat.fontface
INFO [2024-12-20 01:26:32] [1] "plain"
INFO [2024-12-20 01:26:32] 
INFO [2024-12-20 01:26:32] $cat.fontfamily
INFO [2024-12-20 01:26:32] [1] "serif"
INFO [2024-12-20 01:26:32] 
INFO [2024-12-20 01:26:32] $x
INFO [2024-12-20 01:26:32] $x$TF1
INFO [2024-12-20 01:26:32] [1] 3 4 5
INFO [2024-12-20 01:26:32] 
INFO [2024-12-20 01:26:32] $x$TF2
INFO [2024-12-20 01:26:32] [1] 1 2 5
INFO [2024-12-20 01:26:32] 
INFO [2024-12-20 01:26:32] $x$TF3
INFO [2024-12-20 01:26:32] [1] 1 2 5
INFO [2024-12-20 01:26:32] 
INFO [2024-12-20 01:26:32] $x$TF4
INFO [2024-12-20 01:26:32] [1] 1 2 5
INFO [2024-12-20 01:26:32] 
INFO [2024-12-20 01:26:32] 
INFO [2024-12-20 01:26:32] $disable.logging
INFO [2024-12-20 01:26:32] [1] TRUE
INFO [2024-12-20 01:26:32] 
INFO [2024-12-20 01:26:32] $filename
INFO [2024-12-20 01:26:32] NULL
INFO [2024-12-20 01:26:32] 
[ 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 
403.214   8.969 481.662 

Example timings

ChIPpeakAnno.Rcheck/ChIPpeakAnno-Ex.timings

nameusersystemelapsed
ChIPpeakAnno-package0.0010.0010.002
ExonPlusUtr.human.GRCh374.4690.1814.880
HOT.spots0.2030.0190.237
IDRfilter0.0010.0010.003
Peaks.Ste12.Replicate10.1050.0050.113
Peaks.Ste12.Replicate20.0280.0040.032
Peaks.Ste12.Replicate30.0280.0040.034
TSS.human.GRCh370.2680.0300.310
TSS.human.GRCh380.2130.0220.248
TSS.human.NCBI360.1590.0140.181
TSS.mouse.GRCm380.1450.0190.173
TSS.mouse.NCBIM370.1370.0170.164
TSS.rat.RGSC3.40.1120.0140.131
TSS.rat.Rnor_5.00.0990.0120.115
TSS.zebrafish.Zv80.1060.0130.123
TSS.zebrafish.Zv90.1240.0140.144
addAncestors2.2960.1732.649
addGeneIDs4.0431.2235.525
addMetadata3.0960.1633.432
annoGR0.0000.0000.001
annoPeaks6.0910.6327.653
annotatePeakInBatch28.197 1.13731.140
annotatedPeak0.0970.0070.108
assignChromosomeRegion0.0030.0010.004
bdp0.0010.0000.002
binOverFeature1.6500.0321.762
binOverGene0.0010.0010.003
binOverRegions0.0020.0000.004
condenseMatrixByColnames0.0240.0010.026
convert2EntrezID0.8430.0170.897
countPatternInSeqs0.2970.0080.315
cumulativePercentage0.0010.0000.001
downstreams0.0540.0010.058
egOrgMap0.0010.0010.002
enrichedGO0.0040.0030.007
enrichmentPlot1.1560.0181.224
estFragmentLength0.0010.0010.001
estLibSize0.0010.0000.002
featureAlignedDistribution0.5270.0040.559
featureAlignedExtendSignal0.0040.0010.005
featureAlignedHeatmap0.7320.0080.792
featureAlignedSignal0.4500.1510.621
findEnhancers61.331 1.11965.599
findMotifsInPromoterSeqs34.279 0.51836.775
findOverlappingPeaks0.0030.0010.004
findOverlapsOfPeaks4.2980.0374.567
genomicElementDistribution0.0040.0020.005
genomicElementUpSetR0.0020.0010.003
getAllPeakSequence1.0630.0331.158
getAnnotation0.0020.0010.005
getEnrichedGO0.0220.0130.041
getEnrichedPATH0.0020.0010.003
getGO0.0000.0000.001
getGeneSeq0.0020.0020.006
getUniqueGOidCount0.0010.0000.002
getVennCounts0.0020.0010.004
hyperGtest0.0020.0010.003
makeVennDiagram0.0060.0020.007
mergePlusMinusPeaks0.0020.0010.003
metagenePlot4.5780.0754.882
myPeakList0.0210.0040.027
oligoFrequency0.1840.0160.215
oligoSummary0.0010.0010.001
peakPermTest0.0030.0020.006
peaks10.0180.0040.022
peaks20.0160.0030.021
peaks30.0170.0040.021
peaksNearBDP0.0010.0010.002
pie10.0100.0010.015
plotBinOverRegions0.0010.0010.003
preparePool0.0010.0010.002
reCenterPeaks0.0640.0010.068
summarizeOverlapsByBins7.2710.7517.819
summarizePatternInPeaks3.7120.5454.469
tileCount0.7730.6091.000
tileGRanges0.0890.0210.111
toGRanges0.2180.0390.279
translatePattern0.0010.0000.001
wgEncodeTfbsV30.3310.0230.373
write2FASTA0.0380.0080.053
xget0.1900.0210.236