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This page was generated on 2025-04-02 19:28 -0400 (Wed, 02 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.3 (2025-02-28) -- "Trophy Case" 4764
palomino8Windows Server 2022 Datacenterx644.4.3 (2025-02-28 ucrt) -- "Trophy Case" 4495
merida1macOS 12.7.5 Montereyx86_644.4.3 (2025-02-28) -- "Trophy Case" 4522
kjohnson1macOS 13.6.6 Venturaarm644.4.3 (2025-02-28) -- "Trophy Case" 4449
taishanLinux (openEuler 24.03 LTS)aarch644.4.3 (2025-02-28) -- "Trophy Case" 4426
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: 2025-03-31 13:00 -0400 (Mon, 31 Mar 2025)
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 -0400 (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
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for ChIPpeakAnno on nebbiolo2

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: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ChIPpeakAnno_3.40.0.tar.gz
StartedAt: 2025-03-31 20:43:05 -0400 (Mon, 31 Mar 2025)
EndedAt: 2025-03-31 21:07:42 -0400 (Mon, 31 Mar 2025)
EllapsedTime: 1477.5 seconds
RetCode: 0
Status:   OK  
CheckDir: ChIPpeakAnno.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ChIPpeakAnno_3.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/ChIPpeakAnno.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* 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         1.0Mb
    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 loading without being on the library search path ... 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            22.532  0.314  22.847
annotatePeakInBatch      12.574  0.471  13.046
findMotifsInPromoterSeqs 12.703  0.214  12.961
summarizeOverlapsByBins   5.999  0.511   6.243
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/ChIPpeakAnno.Rcheck/00check.log’
for details.


Installation output

ChIPpeakAnno.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL ChIPpeakAnno
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 [2025-03-31 20:52:40] $cat.cex
INFO [2025-03-31 20:52:40] [1] 1
INFO [2025-03-31 20:52:40] 
INFO [2025-03-31 20:52:40] $cat.col
INFO [2025-03-31 20:52:40] [1] "black"
INFO [2025-03-31 20:52:40] 
INFO [2025-03-31 20:52:40] $cat.fontface
INFO [2025-03-31 20:52:40] [1] "plain"
INFO [2025-03-31 20:52:40] 
INFO [2025-03-31 20:52:40] $cat.fontfamily
INFO [2025-03-31 20:52:40] [1] "serif"
INFO [2025-03-31 20:52:40] 
INFO [2025-03-31 20:52:40] $x
INFO [2025-03-31 20:52:40] $x$TF1
INFO [2025-03-31 20:52:40] [1] 3 4 5
INFO [2025-03-31 20:52:40] 
INFO [2025-03-31 20:52:40] $x$TF2
INFO [2025-03-31 20:52:40] [1] 1 2 3 4 5
INFO [2025-03-31 20:52:40] 
INFO [2025-03-31 20:52:40] 
INFO [2025-03-31 20:52:40] $disable.logging
INFO [2025-03-31 20:52:40] [1] TRUE
INFO [2025-03-31 20:52:40] 
INFO [2025-03-31 20:52:40] $filename
INFO [2025-03-31 20:52:40] NULL
INFO [2025-03-31 20:52:40] 
INFO [2025-03-31 20:52:41] $cat.cex
INFO [2025-03-31 20:52:41] [1] 1
INFO [2025-03-31 20:52:41] 
INFO [2025-03-31 20:52:41] $cat.col
INFO [2025-03-31 20:52:41] [1] "black"
INFO [2025-03-31 20:52:41] 
INFO [2025-03-31 20:52:41] $cat.fontface
INFO [2025-03-31 20:52:41] [1] "plain"
INFO [2025-03-31 20:52:41] 
INFO [2025-03-31 20:52:41] $cat.fontfamily
INFO [2025-03-31 20:52:41] [1] "serif"
INFO [2025-03-31 20:52:41] 
INFO [2025-03-31 20:52:41] $x
INFO [2025-03-31 20:52:41] $x$TF1
INFO [2025-03-31 20:52:41] [1] 3 4 5
INFO [2025-03-31 20:52:41] 
INFO [2025-03-31 20:52:41] $x$TF2
INFO [2025-03-31 20:52:41] [1] 1 2 4 5
INFO [2025-03-31 20:52:41] 
INFO [2025-03-31 20:52:41] $x$TF3
INFO [2025-03-31 20:52:41] [1] 3 4 5
INFO [2025-03-31 20:52:41] 
INFO [2025-03-31 20:52:41] $x$TF4
INFO [2025-03-31 20:52:41] [1] 1 2 4 5
INFO [2025-03-31 20:52:41] 
INFO [2025-03-31 20:52:41] 
INFO [2025-03-31 20:52:41] $disable.logging
INFO [2025-03-31 20:52:41] [1] TRUE
INFO [2025-03-31 20:52:41] 
INFO [2025-03-31 20:52:41] $filename
INFO [2025-03-31 20:52:41] NULL
INFO [2025-03-31 20:52:41] 
INFO [2025-03-31 20:52:41] $scaled
INFO [2025-03-31 20:52:41] [1] FALSE
INFO [2025-03-31 20:52:41] 
INFO [2025-03-31 20:52:41] $euler.d
INFO [2025-03-31 20:52:41] [1] FALSE
INFO [2025-03-31 20:52:41] 
INFO [2025-03-31 20:52:41] $cat.cex
INFO [2025-03-31 20:52:41] [1] 1
INFO [2025-03-31 20:52:41] 
INFO [2025-03-31 20:52:41] $cat.col
INFO [2025-03-31 20:52:41] [1] "black"
INFO [2025-03-31 20:52:41] 
INFO [2025-03-31 20:52:41] $cat.fontface
INFO [2025-03-31 20:52:41] [1] "plain"
INFO [2025-03-31 20:52:41] 
INFO [2025-03-31 20:52:41] $cat.fontfamily
INFO [2025-03-31 20:52:41] [1] "serif"
INFO [2025-03-31 20:52:41] 
INFO [2025-03-31 20:52:41] $x
INFO [2025-03-31 20:52:41] $x$TF1
INFO [2025-03-31 20:52:41] [1] 1 2 3
INFO [2025-03-31 20:52:41] 
INFO [2025-03-31 20:52:41] $x$TF2
INFO [2025-03-31 20:52:41] [1] 1 2 3
INFO [2025-03-31 20:52:41] 
INFO [2025-03-31 20:52:41] 
INFO [2025-03-31 20:52:41] $disable.logging
INFO [2025-03-31 20:52:41] [1] TRUE
INFO [2025-03-31 20:52:41] 
INFO [2025-03-31 20:52:41] $filename
INFO [2025-03-31 20:52:41] NULL
INFO [2025-03-31 20:52:41] 
INFO [2025-03-31 20:52:42] $scaled
INFO [2025-03-31 20:52:42] [1] FALSE
INFO [2025-03-31 20:52:42] 
INFO [2025-03-31 20:52:42] $euler.d
INFO [2025-03-31 20:52:42] [1] FALSE
INFO [2025-03-31 20:52:42] 
INFO [2025-03-31 20:52:42] $cat.cex
INFO [2025-03-31 20:52:42] [1] 1
INFO [2025-03-31 20:52:42] 
INFO [2025-03-31 20:52:42] $cat.col
INFO [2025-03-31 20:52:42] [1] "black"
INFO [2025-03-31 20:52:42] 
INFO [2025-03-31 20:52:42] $cat.fontface
INFO [2025-03-31 20:52:42] [1] "plain"
INFO [2025-03-31 20:52:42] 
INFO [2025-03-31 20:52:42] $cat.fontfamily
INFO [2025-03-31 20:52:42] [1] "serif"
INFO [2025-03-31 20:52:42] 
INFO [2025-03-31 20:52:42] $x
INFO [2025-03-31 20:52:42] $x$TF1
INFO [2025-03-31 20:52:42] [1] 4 5 6
INFO [2025-03-31 20:52:42] 
INFO [2025-03-31 20:52:42] $x$TF2
INFO [2025-03-31 20:52:42] [1] 1 2 3
INFO [2025-03-31 20:52:42] 
INFO [2025-03-31 20:52:42] 
INFO [2025-03-31 20:52:42] $disable.logging
INFO [2025-03-31 20:52:42] [1] TRUE
INFO [2025-03-31 20:52:42] 
INFO [2025-03-31 20:52:42] $filename
INFO [2025-03-31 20:52:42] NULL
INFO [2025-03-31 20:52:42] 
INFO [2025-03-31 20:52:42] $scaled
INFO [2025-03-31 20:52:42] [1] FALSE
INFO [2025-03-31 20:52:42] 
INFO [2025-03-31 20:52:42] $euler.d
INFO [2025-03-31 20:52:42] [1] FALSE
INFO [2025-03-31 20:52:42] 
INFO [2025-03-31 20:52:42] $cat.cex
INFO [2025-03-31 20:52:42] [1] 1
INFO [2025-03-31 20:52:42] 
INFO [2025-03-31 20:52:42] $cat.col
INFO [2025-03-31 20:52:42] [1] "black"
INFO [2025-03-31 20:52:42] 
INFO [2025-03-31 20:52:42] $cat.fontface
INFO [2025-03-31 20:52:42] [1] "plain"
INFO [2025-03-31 20:52:42] 
INFO [2025-03-31 20:52:42] $cat.fontfamily
INFO [2025-03-31 20:52:42] [1] "serif"
INFO [2025-03-31 20:52:42] 
INFO [2025-03-31 20:52:42] $x
INFO [2025-03-31 20:52:42] $x$TF1
INFO [2025-03-31 20:52:42] [1] 4 5 6
INFO [2025-03-31 20:52:42] 
INFO [2025-03-31 20:52:42] $x$TF2
INFO [2025-03-31 20:52:42] [1] 1 2 3
INFO [2025-03-31 20:52:42] 
INFO [2025-03-31 20:52:42] 
INFO [2025-03-31 20:52:42] $disable.logging
INFO [2025-03-31 20:52:42] [1] TRUE
INFO [2025-03-31 20:52:42] 
INFO [2025-03-31 20:52:42] $filename
INFO [2025-03-31 20:52:42] NULL
INFO [2025-03-31 20:52:42] 
INFO [2025-03-31 20:52:42] $scaled
INFO [2025-03-31 20:52:42] [1] FALSE
INFO [2025-03-31 20:52:42] 
INFO [2025-03-31 20:52:42] $euler.d
INFO [2025-03-31 20:52:42] [1] FALSE
INFO [2025-03-31 20:52:42] 
INFO [2025-03-31 20:52:42] $cat.cex
INFO [2025-03-31 20:52:42] [1] 1
INFO [2025-03-31 20:52:42] 
INFO [2025-03-31 20:52:42] $cat.col
INFO [2025-03-31 20:52:42] [1] "black"
INFO [2025-03-31 20:52:42] 
INFO [2025-03-31 20:52:42] $cat.fontface
INFO [2025-03-31 20:52:42] [1] "plain"
INFO [2025-03-31 20:52:42] 
INFO [2025-03-31 20:52:42] $cat.fontfamily
INFO [2025-03-31 20:52:42] [1] "serif"
INFO [2025-03-31 20:52:42] 
INFO [2025-03-31 20:52:42] $x
INFO [2025-03-31 20:52:42] $x$TF1
INFO [2025-03-31 20:52:42] [1] 4 5 6
INFO [2025-03-31 20:52:42] 
INFO [2025-03-31 20:52:42] $x$TF2
INFO [2025-03-31 20:52:42] [1] 1 2 3
INFO [2025-03-31 20:52:42] 
INFO [2025-03-31 20:52:42] $x$TF3
INFO [2025-03-31 20:52:42] [1] 2 3 6
INFO [2025-03-31 20:52:42] 
INFO [2025-03-31 20:52:42] 
INFO [2025-03-31 20:52:42] $disable.logging
INFO [2025-03-31 20:52:42] [1] TRUE
INFO [2025-03-31 20:52:42] 
INFO [2025-03-31 20:52:42] $filename
INFO [2025-03-31 20:52:42] NULL
INFO [2025-03-31 20:52:42] 
INFO [2025-03-31 20:52:42] $scaled
INFO [2025-03-31 20:52:42] [1] FALSE
INFO [2025-03-31 20:52:42] 
INFO [2025-03-31 20:52:42] $euler.d
INFO [2025-03-31 20:52:42] [1] FALSE
INFO [2025-03-31 20:52:42] 
INFO [2025-03-31 20:52:42] $cat.cex
INFO [2025-03-31 20:52:42] [1] 1
INFO [2025-03-31 20:52:42] 
INFO [2025-03-31 20:52:42] $cat.col
INFO [2025-03-31 20:52:42] [1] "black"
INFO [2025-03-31 20:52:42] 
INFO [2025-03-31 20:52:42] $cat.fontface
INFO [2025-03-31 20:52:42] [1] "plain"
INFO [2025-03-31 20:52:42] 
INFO [2025-03-31 20:52:42] $cat.fontfamily
INFO [2025-03-31 20:52:42] [1] "serif"
INFO [2025-03-31 20:52:42] 
INFO [2025-03-31 20:52:42] $x
INFO [2025-03-31 20:52:42] $x$TF1
INFO [2025-03-31 20:52:42] [1] 3 4 5
INFO [2025-03-31 20:52:42] 
INFO [2025-03-31 20:52:42] $x$TF2
INFO [2025-03-31 20:52:42] [1] 1 2 5
INFO [2025-03-31 20:52:42] 
INFO [2025-03-31 20:52:42] $x$TF3
INFO [2025-03-31 20:52:42] [1] 1 2 5
INFO [2025-03-31 20:52:42] 
INFO [2025-03-31 20:52:42] 
INFO [2025-03-31 20:52:42] $disable.logging
INFO [2025-03-31 20:52:42] [1] TRUE
INFO [2025-03-31 20:52:42] 
INFO [2025-03-31 20:52:42] $filename
INFO [2025-03-31 20:52:42] NULL
INFO [2025-03-31 20:52:42] 
INFO [2025-03-31 20:52:43] $scaled
INFO [2025-03-31 20:52:43] [1] FALSE
INFO [2025-03-31 20:52:43] 
INFO [2025-03-31 20:52:43] $euler.d
INFO [2025-03-31 20:52:43] [1] FALSE
INFO [2025-03-31 20:52:43] 
INFO [2025-03-31 20:52:43] $cat.cex
INFO [2025-03-31 20:52:43] [1] 1
INFO [2025-03-31 20:52:43] 
INFO [2025-03-31 20:52:43] $cat.col
INFO [2025-03-31 20:52:43] [1] "black"
INFO [2025-03-31 20:52:43] 
INFO [2025-03-31 20:52:43] $cat.fontface
INFO [2025-03-31 20:52:43] [1] "plain"
INFO [2025-03-31 20:52:43] 
INFO [2025-03-31 20:52:43] $cat.fontfamily
INFO [2025-03-31 20:52:43] [1] "serif"
INFO [2025-03-31 20:52:43] 
INFO [2025-03-31 20:52:43] $x
INFO [2025-03-31 20:52:43] $x$TF1
INFO [2025-03-31 20:52:43] [1] 3 4 5
INFO [2025-03-31 20:52:43] 
INFO [2025-03-31 20:52:43] $x$TF2
INFO [2025-03-31 20:52:43] [1] 1 2 5
INFO [2025-03-31 20:52:43] 
INFO [2025-03-31 20:52:43] $x$TF3
INFO [2025-03-31 20:52:43] [1] 1 2 5
INFO [2025-03-31 20:52:43] 
INFO [2025-03-31 20:52:43] $x$TF4
INFO [2025-03-31 20:52:43] [1] 1 2 5
INFO [2025-03-31 20:52:43] 
INFO [2025-03-31 20:52:43] 
INFO [2025-03-31 20:52:43] $disable.logging
INFO [2025-03-31 20:52:43] [1] TRUE
INFO [2025-03-31 20:52:43] 
INFO [2025-03-31 20:52:43] $filename
INFO [2025-03-31 20:52:43] NULL
INFO [2025-03-31 20:52:43] 
[ 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 
158.493   3.704 164.168 

Example timings

ChIPpeakAnno.Rcheck/ChIPpeakAnno-Ex.timings

nameusersystemelapsed
ChIPpeakAnno-package0.0010.0000.001
ExonPlusUtr.human.GRCh373.6390.2313.870
HOT.spots0.1350.0160.151
IDRfilter0.0000.0000.001
Peaks.Ste12.Replicate10.0460.0050.050
Peaks.Ste12.Replicate20.0100.0010.011
Peaks.Ste12.Replicate30.0090.0010.010
TSS.human.GRCh370.1880.0140.202
TSS.human.GRCh380.1450.0020.147
TSS.human.NCBI360.1060.0080.113
TSS.mouse.GRCm380.1050.0050.110
TSS.mouse.NCBIM370.0940.0040.098
TSS.rat.RGSC3.40.0730.0070.080
TSS.rat.Rnor_5.00.0630.0060.068
TSS.zebrafish.Zv80.0690.0060.074
TSS.zebrafish.Zv90.0800.0050.087
addAncestors0.9260.0230.949
addGeneIDs0.8590.0480.909
addMetadata1.0240.0811.105
annoGR000
annoPeaks3.0940.1823.958
annotatePeakInBatch12.574 0.47113.046
annotatedPeak0.0610.0000.060
assignChromosomeRegion0.0010.0000.001
bdp0.0010.0000.000
binOverFeature0.7010.0090.710
binOverGene0.0010.0000.000
binOverRegions0.0000.0000.001
condenseMatrixByColnames0.010.000.01
convert2EntrezID0.4380.0030.440
countPatternInSeqs0.1610.0010.163
cumulativePercentage000
downstreams0.0210.0000.021
egOrgMap000
enrichedGO0.0020.0000.002
enrichmentPlot0.4610.0030.463
estFragmentLength000
estLibSize000
featureAlignedDistribution0.2080.0020.210
featureAlignedExtendSignal0.0000.0000.001
featureAlignedHeatmap0.2900.0000.291
featureAlignedSignal0.1620.0180.181
findEnhancers22.532 0.31422.847
findMotifsInPromoterSeqs12.703 0.21412.961
findOverlappingPeaks0.0010.0000.000
findOverlapsOfPeaks1.6310.0021.633
genomicElementDistribution0.0000.0010.001
genomicElementUpSetR000
getAllPeakSequence0.5110.0030.515
getAnnotation0.0000.0000.001
getEnrichedGO0.0080.0000.008
getEnrichedPATH0.0010.0000.000
getGO0.0000.0000.001
getGeneSeq0.0000.0000.001
getUniqueGOidCount0.0000.0000.001
getVennCounts0.0000.0000.001
hyperGtest0.0000.0000.001
makeVennDiagram0.0020.0000.002
mergePlusMinusPeaks000
metagenePlot1.8530.0281.882
myPeakList0.0140.0010.016
oligoFrequency0.0910.0010.092
oligoSummary0.0000.0000.001
peakPermTest0.0010.0000.001
peaks10.0060.0000.007
peaks20.0060.0000.007
peaks30.0060.0000.006
peaksNearBDP000
pie10.0040.0010.005
plotBinOverRegions0.0000.0000.001
preparePool000
reCenterPeaks0.0210.0000.021
summarizeOverlapsByBins5.9990.5116.243
summarizePatternInPeaks1.2360.1181.355
tileCount0.1950.1890.343
tileGRanges0.0330.0040.038
toGRanges0.1780.1530.080
translatePattern0.0010.0000.001
wgEncodeTfbsV30.2190.0080.227
write2FASTA0.0120.0030.015
xget0.1090.0040.113