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This page was generated on 2024-02-22 12:48:03 -0500 (Thu, 22 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4657
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4397
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Package 333/2244HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPpeakAnno 3.37.4  (landing page)
Jianhong Ou
Snapshot Date: 2024-02-21 14:10:10 -0500 (Wed, 21 Feb 2024)
git_url: https://git.bioconductor.org/packages/ChIPpeakAnno
git_branch: devel
git_last_commit: 58a122c
git_last_commit_date: 2024-01-29 08:57:31 -0500 (Mon, 29 Jan 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for ChIPpeakAnno on nebbiolo1


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: 3.37.4
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ChIPpeakAnno_3.37.4.tar.gz
StartedAt: 2024-02-21 21:28:41 -0500 (Wed, 21 Feb 2024)
EndedAt: 2024-02-21 21:53:33 -0500 (Wed, 21 Feb 2024)
EllapsedTime: 1491.9 seconds
RetCode: 0
Status:   OK  
CheckDir: ChIPpeakAnno.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ChIPpeakAnno_3.37.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/ChIPpeakAnno.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘ChIPpeakAnno/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChIPpeakAnno’ version ‘3.37.4’
* 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 19.1Mb
  sub-directories of 1Mb or more:
    data     12.6Mb
    extdata   5.2Mb
* 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 R 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            23.209  0.575  23.787
annotatePeakInBatch      12.771  1.316  14.087
findMotifsInPromoterSeqs 13.283  0.304  13.587
summarizeOverlapsByBins   4.987  0.466   5.174
* 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-3.19-bioc/meat/ChIPpeakAnno.Rcheck/00check.log’
for details.



Installation output

ChIPpeakAnno.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL ChIPpeakAnno
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-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 Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
Copyright (C) 2024 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, 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 [2024-02-21 21:38:23] $cat.cex
INFO [2024-02-21 21:38:23] [1] 1
INFO [2024-02-21 21:38:23] 
INFO [2024-02-21 21:38:23] $cat.col
INFO [2024-02-21 21:38:23] [1] "black"
INFO [2024-02-21 21:38:23] 
INFO [2024-02-21 21:38:23] $cat.fontface
INFO [2024-02-21 21:38:23] [1] "plain"
INFO [2024-02-21 21:38:23] 
INFO [2024-02-21 21:38:23] $cat.fontfamily
INFO [2024-02-21 21:38:23] [1] "serif"
INFO [2024-02-21 21:38:23] 
INFO [2024-02-21 21:38:23] $x
INFO [2024-02-21 21:38:23] $x$TF1
INFO [2024-02-21 21:38:23] [1] 3 4 5
INFO [2024-02-21 21:38:23] 
INFO [2024-02-21 21:38:23] $x$TF2
INFO [2024-02-21 21:38:23] [1] 1 2 3 4 5
INFO [2024-02-21 21:38:23] 
INFO [2024-02-21 21:38:23] 
INFO [2024-02-21 21:38:23] $disable.logging
INFO [2024-02-21 21:38:23] [1] TRUE
INFO [2024-02-21 21:38:23] 
INFO [2024-02-21 21:38:23] $filename
INFO [2024-02-21 21:38:23] NULL
INFO [2024-02-21 21:38:23] 
INFO [2024-02-21 21:38:23] $cat.cex
INFO [2024-02-21 21:38:23] [1] 1
INFO [2024-02-21 21:38:23] 
INFO [2024-02-21 21:38:23] $cat.col
INFO [2024-02-21 21:38:23] [1] "black"
INFO [2024-02-21 21:38:23] 
INFO [2024-02-21 21:38:23] $cat.fontface
INFO [2024-02-21 21:38:23] [1] "plain"
INFO [2024-02-21 21:38:23] 
INFO [2024-02-21 21:38:23] $cat.fontfamily
INFO [2024-02-21 21:38:23] [1] "serif"
INFO [2024-02-21 21:38:23] 
INFO [2024-02-21 21:38:23] $x
INFO [2024-02-21 21:38:23] $x$TF1
INFO [2024-02-21 21:38:23] [1] 3 4 5
INFO [2024-02-21 21:38:23] 
INFO [2024-02-21 21:38:23] $x$TF2
INFO [2024-02-21 21:38:23] [1] 1 2 4 5
INFO [2024-02-21 21:38:23] 
INFO [2024-02-21 21:38:23] $x$TF3
INFO [2024-02-21 21:38:23] [1] 3 4 5
INFO [2024-02-21 21:38:23] 
INFO [2024-02-21 21:38:23] $x$TF4
INFO [2024-02-21 21:38:23] [1] 1 2 4 5
INFO [2024-02-21 21:38:23] 
INFO [2024-02-21 21:38:23] 
INFO [2024-02-21 21:38:23] $disable.logging
INFO [2024-02-21 21:38:23] [1] TRUE
INFO [2024-02-21 21:38:23] 
INFO [2024-02-21 21:38:23] $filename
INFO [2024-02-21 21:38:23] NULL
INFO [2024-02-21 21:38:23] 
INFO [2024-02-21 21:38:23] $scaled
INFO [2024-02-21 21:38:23] [1] FALSE
INFO [2024-02-21 21:38:23] 
INFO [2024-02-21 21:38:23] $euler.d
INFO [2024-02-21 21:38:23] [1] FALSE
INFO [2024-02-21 21:38:23] 
INFO [2024-02-21 21:38:23] $cat.cex
INFO [2024-02-21 21:38:23] [1] 1
INFO [2024-02-21 21:38:23] 
INFO [2024-02-21 21:38:23] $cat.col
INFO [2024-02-21 21:38:23] [1] "black"
INFO [2024-02-21 21:38:23] 
INFO [2024-02-21 21:38:23] $cat.fontface
INFO [2024-02-21 21:38:23] [1] "plain"
INFO [2024-02-21 21:38:23] 
INFO [2024-02-21 21:38:23] $cat.fontfamily
INFO [2024-02-21 21:38:23] [1] "serif"
INFO [2024-02-21 21:38:23] 
INFO [2024-02-21 21:38:23] $x
INFO [2024-02-21 21:38:23] $x$TF1
INFO [2024-02-21 21:38:23] [1] 1 2 3
INFO [2024-02-21 21:38:23] 
INFO [2024-02-21 21:38:23] $x$TF2
INFO [2024-02-21 21:38:23] [1] 1 2 3
INFO [2024-02-21 21:38:23] 
INFO [2024-02-21 21:38:23] 
INFO [2024-02-21 21:38:23] $disable.logging
INFO [2024-02-21 21:38:23] [1] TRUE
INFO [2024-02-21 21:38:23] 
INFO [2024-02-21 21:38:23] $filename
INFO [2024-02-21 21:38:23] NULL
INFO [2024-02-21 21:38:23] 
INFO [2024-02-21 21:38:23] $scaled
INFO [2024-02-21 21:38:23] [1] FALSE
INFO [2024-02-21 21:38:23] 
INFO [2024-02-21 21:38:23] $euler.d
INFO [2024-02-21 21:38:23] [1] FALSE
INFO [2024-02-21 21:38:23] 
INFO [2024-02-21 21:38:23] $cat.cex
INFO [2024-02-21 21:38:23] [1] 1
INFO [2024-02-21 21:38:23] 
INFO [2024-02-21 21:38:23] $cat.col
INFO [2024-02-21 21:38:23] [1] "black"
INFO [2024-02-21 21:38:23] 
INFO [2024-02-21 21:38:23] $cat.fontface
INFO [2024-02-21 21:38:23] [1] "plain"
INFO [2024-02-21 21:38:23] 
INFO [2024-02-21 21:38:23] $cat.fontfamily
INFO [2024-02-21 21:38:23] [1] "serif"
INFO [2024-02-21 21:38:23] 
INFO [2024-02-21 21:38:23] $x
INFO [2024-02-21 21:38:23] $x$TF1
INFO [2024-02-21 21:38:23] [1] 4 5 6
INFO [2024-02-21 21:38:23] 
INFO [2024-02-21 21:38:23] $x$TF2
INFO [2024-02-21 21:38:23] [1] 1 2 3
INFO [2024-02-21 21:38:23] 
INFO [2024-02-21 21:38:23] 
INFO [2024-02-21 21:38:23] $disable.logging
INFO [2024-02-21 21:38:23] [1] TRUE
INFO [2024-02-21 21:38:23] 
INFO [2024-02-21 21:38:23] $filename
INFO [2024-02-21 21:38:23] NULL
INFO [2024-02-21 21:38:23] 
INFO [2024-02-21 21:38:24] $scaled
INFO [2024-02-21 21:38:24] [1] FALSE
INFO [2024-02-21 21:38:24] 
INFO [2024-02-21 21:38:24] $euler.d
INFO [2024-02-21 21:38:24] [1] FALSE
INFO [2024-02-21 21:38:24] 
INFO [2024-02-21 21:38:24] $cat.cex
INFO [2024-02-21 21:38:24] [1] 1
INFO [2024-02-21 21:38:24] 
INFO [2024-02-21 21:38:24] $cat.col
INFO [2024-02-21 21:38:24] [1] "black"
INFO [2024-02-21 21:38:24] 
INFO [2024-02-21 21:38:24] $cat.fontface
INFO [2024-02-21 21:38:24] [1] "plain"
INFO [2024-02-21 21:38:24] 
INFO [2024-02-21 21:38:24] $cat.fontfamily
INFO [2024-02-21 21:38:24] [1] "serif"
INFO [2024-02-21 21:38:24] 
INFO [2024-02-21 21:38:24] $x
INFO [2024-02-21 21:38:24] $x$TF1
INFO [2024-02-21 21:38:24] [1] 4 5 6
INFO [2024-02-21 21:38:24] 
INFO [2024-02-21 21:38:24] $x$TF2
INFO [2024-02-21 21:38:24] [1] 1 2 3
INFO [2024-02-21 21:38:24] 
INFO [2024-02-21 21:38:24] 
INFO [2024-02-21 21:38:24] $disable.logging
INFO [2024-02-21 21:38:24] [1] TRUE
INFO [2024-02-21 21:38:24] 
INFO [2024-02-21 21:38:24] $filename
INFO [2024-02-21 21:38:24] NULL
INFO [2024-02-21 21:38:24] 
INFO [2024-02-21 21:38:24] $scaled
INFO [2024-02-21 21:38:24] [1] FALSE
INFO [2024-02-21 21:38:24] 
INFO [2024-02-21 21:38:24] $euler.d
INFO [2024-02-21 21:38:24] [1] FALSE
INFO [2024-02-21 21:38:24] 
INFO [2024-02-21 21:38:24] $cat.cex
INFO [2024-02-21 21:38:24] [1] 1
INFO [2024-02-21 21:38:24] 
INFO [2024-02-21 21:38:24] $cat.col
INFO [2024-02-21 21:38:24] [1] "black"
INFO [2024-02-21 21:38:24] 
INFO [2024-02-21 21:38:24] $cat.fontface
INFO [2024-02-21 21:38:24] [1] "plain"
INFO [2024-02-21 21:38:24] 
INFO [2024-02-21 21:38:24] $cat.fontfamily
INFO [2024-02-21 21:38:24] [1] "serif"
INFO [2024-02-21 21:38:24] 
INFO [2024-02-21 21:38:24] $x
INFO [2024-02-21 21:38:24] $x$TF1
INFO [2024-02-21 21:38:24] [1] 4 5 6
INFO [2024-02-21 21:38:24] 
INFO [2024-02-21 21:38:24] $x$TF2
INFO [2024-02-21 21:38:24] [1] 1 2 3
INFO [2024-02-21 21:38:24] 
INFO [2024-02-21 21:38:24] $x$TF3
INFO [2024-02-21 21:38:24] [1] 2 3 6
INFO [2024-02-21 21:38:24] 
INFO [2024-02-21 21:38:24] 
INFO [2024-02-21 21:38:24] $disable.logging
INFO [2024-02-21 21:38:24] [1] TRUE
INFO [2024-02-21 21:38:24] 
INFO [2024-02-21 21:38:24] $filename
INFO [2024-02-21 21:38:24] NULL
INFO [2024-02-21 21:38:24] 
INFO [2024-02-21 21:38:24] $scaled
INFO [2024-02-21 21:38:24] [1] FALSE
INFO [2024-02-21 21:38:24] 
INFO [2024-02-21 21:38:24] $euler.d
INFO [2024-02-21 21:38:24] [1] FALSE
INFO [2024-02-21 21:38:24] 
INFO [2024-02-21 21:38:24] $cat.cex
INFO [2024-02-21 21:38:24] [1] 1
INFO [2024-02-21 21:38:24] 
INFO [2024-02-21 21:38:24] $cat.col
INFO [2024-02-21 21:38:24] [1] "black"
INFO [2024-02-21 21:38:24] 
INFO [2024-02-21 21:38:24] $cat.fontface
INFO [2024-02-21 21:38:24] [1] "plain"
INFO [2024-02-21 21:38:24] 
INFO [2024-02-21 21:38:24] $cat.fontfamily
INFO [2024-02-21 21:38:24] [1] "serif"
INFO [2024-02-21 21:38:24] 
INFO [2024-02-21 21:38:24] $x
INFO [2024-02-21 21:38:24] $x$TF1
INFO [2024-02-21 21:38:24] [1] 3 4 5
INFO [2024-02-21 21:38:24] 
INFO [2024-02-21 21:38:24] $x$TF2
INFO [2024-02-21 21:38:24] [1] 1 2 5
INFO [2024-02-21 21:38:24] 
INFO [2024-02-21 21:38:24] $x$TF3
INFO [2024-02-21 21:38:24] [1] 1 2 5
INFO [2024-02-21 21:38:24] 
INFO [2024-02-21 21:38:24] 
INFO [2024-02-21 21:38:24] $disable.logging
INFO [2024-02-21 21:38:24] [1] TRUE
INFO [2024-02-21 21:38:24] 
INFO [2024-02-21 21:38:24] $filename
INFO [2024-02-21 21:38:24] NULL
INFO [2024-02-21 21:38:24] 
INFO [2024-02-21 21:38:25] $scaled
INFO [2024-02-21 21:38:25] [1] FALSE
INFO [2024-02-21 21:38:25] 
INFO [2024-02-21 21:38:25] $euler.d
INFO [2024-02-21 21:38:25] [1] FALSE
INFO [2024-02-21 21:38:25] 
INFO [2024-02-21 21:38:25] $cat.cex
INFO [2024-02-21 21:38:25] [1] 1
INFO [2024-02-21 21:38:25] 
INFO [2024-02-21 21:38:25] $cat.col
INFO [2024-02-21 21:38:25] [1] "black"
INFO [2024-02-21 21:38:25] 
INFO [2024-02-21 21:38:25] $cat.fontface
INFO [2024-02-21 21:38:25] [1] "plain"
INFO [2024-02-21 21:38:25] 
INFO [2024-02-21 21:38:25] $cat.fontfamily
INFO [2024-02-21 21:38:25] [1] "serif"
INFO [2024-02-21 21:38:25] 
INFO [2024-02-21 21:38:25] $x
INFO [2024-02-21 21:38:25] $x$TF1
INFO [2024-02-21 21:38:25] [1] 3 4 5
INFO [2024-02-21 21:38:25] 
INFO [2024-02-21 21:38:25] $x$TF2
INFO [2024-02-21 21:38:25] [1] 1 2 5
INFO [2024-02-21 21:38:25] 
INFO [2024-02-21 21:38:25] $x$TF3
INFO [2024-02-21 21:38:25] [1] 1 2 5
INFO [2024-02-21 21:38:25] 
INFO [2024-02-21 21:38:25] $x$TF4
INFO [2024-02-21 21:38:25] [1] 1 2 5
INFO [2024-02-21 21:38:25] 
INFO [2024-02-21 21:38:25] 
INFO [2024-02-21 21:38:25] $disable.logging
INFO [2024-02-21 21:38:25] [1] TRUE
INFO [2024-02-21 21:38:25] 
INFO [2024-02-21 21:38:25] $filename
INFO [2024-02-21 21:38:25] NULL
INFO [2024-02-21 21:38:25] 
[ 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 
157.399   6.072 165.976 

Example timings

ChIPpeakAnno.Rcheck/ChIPpeakAnno-Ex.timings

nameusersystemelapsed
ChIPpeakAnno-package000
ExonPlusUtr.human.GRCh373.2230.1873.411
HOT.spots0.1210.0280.149
IDRfilter0.0010.0000.001
Peaks.Ste12.Replicate10.0470.0080.055
Peaks.Ste12.Replicate20.0130.0000.013
Peaks.Ste12.Replicate30.0120.0000.013
TSS.human.GRCh370.1690.0240.193
TSS.human.GRCh380.1470.0050.151
TSS.human.NCBI360.1090.0150.124
TSS.mouse.GRCm380.0990.0080.107
TSS.mouse.NCBIM370.0910.0080.099
TSS.rat.RGSC3.40.0810.0040.085
TSS.rat.Rnor_5.00.0680.0070.075
TSS.zebrafish.Zv80.0740.0030.078
TSS.zebrafish.Zv90.0810.0080.090
addAncestors0.9790.0881.068
addGeneIDs0.7810.0610.843
addMetadata1.2130.1161.329
annoGR000
annoPeaks2.6950.4374.377
annotatePeakInBatch12.771 1.31614.087
annotatedPeak0.0600.0030.063
assignChromosomeRegion0.0010.0000.001
bdp0.0000.0000.001
binOverFeature0.6830.0070.692
binOverGene0.0000.0000.001
binOverRegions0.0000.0000.001
condenseMatrixByColnames0.010.000.01
convert2EntrezID0.3170.0150.333
countPatternInSeqs0.2200.0130.233
cumulativePercentage000
downstreams0.0220.0000.023
egOrgMap0.0010.0000.000
enrichedGO0.0030.0000.002
enrichmentPlot0.4840.0070.492
estFragmentLength0.0010.0000.000
estLibSize0.0010.0010.000
featureAlignedDistribution0.2170.0230.241
featureAlignedExtendSignal0.0010.0000.002
featureAlignedHeatmap0.4180.0350.454
featureAlignedSignal0.2180.0650.282
findEnhancers23.209 0.57523.787
findMotifsInPromoterSeqs13.283 0.30413.587
findOverlappingPeaks0.0000.0010.001
findOverlapsOfPeaks1.6990.0101.710
genomicElementDistribution0.0020.0000.001
genomicElementUpSetR0.0010.0000.000
getAllPeakSequence0.6590.0040.662
getAnnotation0.0010.0000.001
getEnrichedGO0.0100.0000.011
getEnrichedPATH0.0010.0000.000
getGO0.0010.0000.000
getGeneSeq0.0010.0000.001
getUniqueGOidCount0.0010.0000.001
getVennCounts0.0010.0010.001
hyperGtest0.0000.0010.002
makeVennDiagram0.0010.0010.003
mergePlusMinusPeaks0.0010.0000.001
metagenePlot1.9250.0241.951
myPeakList0.0170.0000.017
oligoFrequency0.1030.0040.107
oligoSummary0.0010.0000.000
peakPermTest0.0010.0000.002
peaks10.0080.0000.008
peaks20.0070.0000.007
peaks30.0060.0000.007
peaksNearBDP0.0010.0000.001
pie10.0050.0000.004
plotBinOverRegions0.0000.0000.001
preparePool0.0000.0000.001
reCenterPeaks0.0210.0000.022
summarizeOverlapsByBins4.9870.4665.174
summarizePatternInPeaks1.3420.1571.498
tileCount0.1650.1800.302
tileGRanges0.0980.1170.034
toGRanges0.0660.0110.078
translatePattern0.0010.0010.000
wgEncodeTfbsV30.2370.0040.241
write2FASTA0.0160.0000.016
xget0.1170.0080.126