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This page was generated on 2024-02-21 11:35:55 -0500 (Wed, 21 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4691
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4444
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4465
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 333/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPpeakAnno 3.36.1  (landing page)
Jianhong Ou
Snapshot Date: 2024-02-20 14:05:06 -0500 (Tue, 20 Feb 2024)
git_url: https://git.bioconductor.org/packages/ChIPpeakAnno
git_branch: RELEASE_3_18
git_last_commit: 105ec60
git_last_commit_date: 2024-02-15 15:06:09 -0500 (Thu, 15 Feb 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

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: 3.36.1
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings ChIPpeakAnno_3.36.1.tar.gz
StartedAt: 2024-02-20 20:59:26 -0500 (Tue, 20 Feb 2024)
EndedAt: 2024-02-20 21:15:17 -0500 (Tue, 20 Feb 2024)
EllapsedTime: 951.1 seconds
RetCode: 0
Status:   OK  
CheckDir: ChIPpeakAnno.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings ChIPpeakAnno_3.36.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/ChIPpeakAnno.Rcheck’
* using R version 4.3.2 Patched (2023-11-13 r85521)
* using platform: x86_64-pc-linux-gnu (64-bit)
* 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 ‘3.36.1’
* 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 ... NOTE
Namespace in Imports field not imported from: ‘ensembldb’
  All declared Imports should be used.
* 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 ... NOTE
checkRd: (-1) assignChromosomeRegion.Rd:133: Escaped LaTeX specials: \_
* 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            23.598  0.536  24.133
annotatePeakInBatch      13.372  1.144  14.516
findMotifsInPromoterSeqs 12.908  0.216  13.133
summarizeOverlapsByBins   4.973  0.509   5.217
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘ChIPpeakAnno.Rmd’ using ‘UTF-8’... OK
  ‘FAQs.Rmd’ using ‘UTF-8’... OK
  ‘pipeline.Rmd’ using ‘UTF-8’... OK
  ‘quickStart.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/ChIPpeakAnno.Rcheck/00check.log’
for details.



Installation output

ChIPpeakAnno.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL ChIPpeakAnno
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-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
in method for ‘annoGR’ with signature ‘"EnsDb"’: no definition for class “EnsDb”
in method for ‘toGRanges’ with signature ‘"EnsDb"’: no definition for class “EnsDb”
** 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 4.3.2 Patched (2023-11-13 r85521) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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, sort, 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("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 [2024-02-20 21:08:39] $cat.cex
INFO [2024-02-20 21:08:39] [1] 1
INFO [2024-02-20 21:08:39] 
INFO [2024-02-20 21:08:39] $cat.col
INFO [2024-02-20 21:08:39] [1] "black"
INFO [2024-02-20 21:08:39] 
INFO [2024-02-20 21:08:39] $cat.fontface
INFO [2024-02-20 21:08:39] [1] "plain"
INFO [2024-02-20 21:08:39] 
INFO [2024-02-20 21:08:39] $cat.fontfamily
INFO [2024-02-20 21:08:39] [1] "serif"
INFO [2024-02-20 21:08:39] 
INFO [2024-02-20 21:08:39] $x
INFO [2024-02-20 21:08:39] $x$TF1
INFO [2024-02-20 21:08:39] [1] 3 4 5
INFO [2024-02-20 21:08:39] 
INFO [2024-02-20 21:08:39] $x$TF2
INFO [2024-02-20 21:08:39] [1] 1 2 3 4 5
INFO [2024-02-20 21:08:39] 
INFO [2024-02-20 21:08:39] 
INFO [2024-02-20 21:08:39] $filename
INFO [2024-02-20 21:08:39] NULL
INFO [2024-02-20 21:08:39] 
INFO [2024-02-20 21:08:39] $disable.logging
INFO [2024-02-20 21:08:39] [1] TRUE
INFO [2024-02-20 21:08:39] 
INFO [2024-02-20 21:08:40] $cat.cex
INFO [2024-02-20 21:08:40] [1] 1
INFO [2024-02-20 21:08:40] 
INFO [2024-02-20 21:08:40] $cat.col
INFO [2024-02-20 21:08:40] [1] "black"
INFO [2024-02-20 21:08:40] 
INFO [2024-02-20 21:08:40] $cat.fontface
INFO [2024-02-20 21:08:40] [1] "plain"
INFO [2024-02-20 21:08:40] 
INFO [2024-02-20 21:08:40] $cat.fontfamily
INFO [2024-02-20 21:08:40] [1] "serif"
INFO [2024-02-20 21:08:40] 
INFO [2024-02-20 21:08:40] $x
INFO [2024-02-20 21:08:40] $x$TF1
INFO [2024-02-20 21:08:40] [1] 3 4 5
INFO [2024-02-20 21:08:40] 
INFO [2024-02-20 21:08:40] $x$TF2
INFO [2024-02-20 21:08:40] [1] 1 2 4 5
INFO [2024-02-20 21:08:40] 
INFO [2024-02-20 21:08:40] $x$TF3
INFO [2024-02-20 21:08:40] [1] 3 4 5
INFO [2024-02-20 21:08:40] 
INFO [2024-02-20 21:08:40] $x$TF4
INFO [2024-02-20 21:08:40] [1] 1 2 4 5
INFO [2024-02-20 21:08:40] 
INFO [2024-02-20 21:08:40] 
INFO [2024-02-20 21:08:40] $filename
INFO [2024-02-20 21:08:40] NULL
INFO [2024-02-20 21:08:40] 
INFO [2024-02-20 21:08:40] $disable.logging
INFO [2024-02-20 21:08:40] [1] TRUE
INFO [2024-02-20 21:08:40] 
INFO [2024-02-20 21:08:40] $scaled
INFO [2024-02-20 21:08:40] [1] FALSE
INFO [2024-02-20 21:08:40] 
INFO [2024-02-20 21:08:40] $euler.d
INFO [2024-02-20 21:08:40] [1] FALSE
INFO [2024-02-20 21:08:40] 
INFO [2024-02-20 21:08:40] $cat.cex
INFO [2024-02-20 21:08:40] [1] 1
INFO [2024-02-20 21:08:40] 
INFO [2024-02-20 21:08:40] $cat.col
INFO [2024-02-20 21:08:40] [1] "black"
INFO [2024-02-20 21:08:40] 
INFO [2024-02-20 21:08:40] $cat.fontface
INFO [2024-02-20 21:08:40] [1] "plain"
INFO [2024-02-20 21:08:40] 
INFO [2024-02-20 21:08:40] $cat.fontfamily
INFO [2024-02-20 21:08:40] [1] "serif"
INFO [2024-02-20 21:08:40] 
INFO [2024-02-20 21:08:40] $x
INFO [2024-02-20 21:08:40] $x$TF1
INFO [2024-02-20 21:08:40] [1] 1 2 3
INFO [2024-02-20 21:08:40] 
INFO [2024-02-20 21:08:40] $x$TF2
INFO [2024-02-20 21:08:40] [1] 1 2 3
INFO [2024-02-20 21:08:40] 
INFO [2024-02-20 21:08:40] 
INFO [2024-02-20 21:08:40] $filename
INFO [2024-02-20 21:08:40] NULL
INFO [2024-02-20 21:08:40] 
INFO [2024-02-20 21:08:40] $disable.logging
INFO [2024-02-20 21:08:40] [1] TRUE
INFO [2024-02-20 21:08:40] 
INFO [2024-02-20 21:08:40] $scaled
INFO [2024-02-20 21:08:40] [1] FALSE
INFO [2024-02-20 21:08:40] 
INFO [2024-02-20 21:08:40] $euler.d
INFO [2024-02-20 21:08:40] [1] FALSE
INFO [2024-02-20 21:08:40] 
INFO [2024-02-20 21:08:40] $cat.cex
INFO [2024-02-20 21:08:40] [1] 1
INFO [2024-02-20 21:08:40] 
INFO [2024-02-20 21:08:40] $cat.col
INFO [2024-02-20 21:08:40] [1] "black"
INFO [2024-02-20 21:08:40] 
INFO [2024-02-20 21:08:40] $cat.fontface
INFO [2024-02-20 21:08:40] [1] "plain"
INFO [2024-02-20 21:08:40] 
INFO [2024-02-20 21:08:40] $cat.fontfamily
INFO [2024-02-20 21:08:40] [1] "serif"
INFO [2024-02-20 21:08:40] 
INFO [2024-02-20 21:08:40] $x
INFO [2024-02-20 21:08:40] $x$TF1
INFO [2024-02-20 21:08:40] [1] 4 5 6
INFO [2024-02-20 21:08:40] 
INFO [2024-02-20 21:08:40] $x$TF2
INFO [2024-02-20 21:08:40] [1] 1 2 3
INFO [2024-02-20 21:08:40] 
INFO [2024-02-20 21:08:40] 
INFO [2024-02-20 21:08:40] $filename
INFO [2024-02-20 21:08:40] NULL
INFO [2024-02-20 21:08:40] 
INFO [2024-02-20 21:08:40] $disable.logging
INFO [2024-02-20 21:08:40] [1] TRUE
INFO [2024-02-20 21:08:40] 
INFO [2024-02-20 21:08:41] $scaled
INFO [2024-02-20 21:08:41] [1] FALSE
INFO [2024-02-20 21:08:41] 
INFO [2024-02-20 21:08:41] $euler.d
INFO [2024-02-20 21:08:41] [1] FALSE
INFO [2024-02-20 21:08:41] 
INFO [2024-02-20 21:08:41] $cat.cex
INFO [2024-02-20 21:08:41] [1] 1
INFO [2024-02-20 21:08:41] 
INFO [2024-02-20 21:08:41] $cat.col
INFO [2024-02-20 21:08:41] [1] "black"
INFO [2024-02-20 21:08:41] 
INFO [2024-02-20 21:08:41] $cat.fontface
INFO [2024-02-20 21:08:41] [1] "plain"
INFO [2024-02-20 21:08:41] 
INFO [2024-02-20 21:08:41] $cat.fontfamily
INFO [2024-02-20 21:08:41] [1] "serif"
INFO [2024-02-20 21:08:41] 
INFO [2024-02-20 21:08:41] $x
INFO [2024-02-20 21:08:41] $x$TF1
INFO [2024-02-20 21:08:41] [1] 4 5 6
INFO [2024-02-20 21:08:41] 
INFO [2024-02-20 21:08:41] $x$TF2
INFO [2024-02-20 21:08:41] [1] 1 2 3
INFO [2024-02-20 21:08:41] 
INFO [2024-02-20 21:08:41] 
INFO [2024-02-20 21:08:41] $filename
INFO [2024-02-20 21:08:41] NULL
INFO [2024-02-20 21:08:41] 
INFO [2024-02-20 21:08:41] $disable.logging
INFO [2024-02-20 21:08:41] [1] TRUE
INFO [2024-02-20 21:08:41] 
INFO [2024-02-20 21:08:41] $scaled
INFO [2024-02-20 21:08:41] [1] FALSE
INFO [2024-02-20 21:08:41] 
INFO [2024-02-20 21:08:41] $euler.d
INFO [2024-02-20 21:08:41] [1] FALSE
INFO [2024-02-20 21:08:41] 
INFO [2024-02-20 21:08:41] $cat.cex
INFO [2024-02-20 21:08:41] [1] 1
INFO [2024-02-20 21:08:41] 
INFO [2024-02-20 21:08:41] $cat.col
INFO [2024-02-20 21:08:41] [1] "black"
INFO [2024-02-20 21:08:41] 
INFO [2024-02-20 21:08:41] $cat.fontface
INFO [2024-02-20 21:08:41] [1] "plain"
INFO [2024-02-20 21:08:41] 
INFO [2024-02-20 21:08:41] $cat.fontfamily
INFO [2024-02-20 21:08:41] [1] "serif"
INFO [2024-02-20 21:08:41] 
INFO [2024-02-20 21:08:41] $x
INFO [2024-02-20 21:08:41] $x$TF1
INFO [2024-02-20 21:08:41] [1] 4 5 6
INFO [2024-02-20 21:08:41] 
INFO [2024-02-20 21:08:41] $x$TF2
INFO [2024-02-20 21:08:41] [1] 1 2 3
INFO [2024-02-20 21:08:41] 
INFO [2024-02-20 21:08:41] $x$TF3
INFO [2024-02-20 21:08:41] [1] 2 3 6
INFO [2024-02-20 21:08:41] 
INFO [2024-02-20 21:08:41] 
INFO [2024-02-20 21:08:41] $filename
INFO [2024-02-20 21:08:41] NULL
INFO [2024-02-20 21:08:41] 
INFO [2024-02-20 21:08:41] $disable.logging
INFO [2024-02-20 21:08:41] [1] TRUE
INFO [2024-02-20 21:08:41] 
INFO [2024-02-20 21:08:41] $scaled
INFO [2024-02-20 21:08:41] [1] FALSE
INFO [2024-02-20 21:08:41] 
INFO [2024-02-20 21:08:41] $euler.d
INFO [2024-02-20 21:08:41] [1] FALSE
INFO [2024-02-20 21:08:41] 
INFO [2024-02-20 21:08:41] $cat.cex
INFO [2024-02-20 21:08:41] [1] 1
INFO [2024-02-20 21:08:41] 
INFO [2024-02-20 21:08:41] $cat.col
INFO [2024-02-20 21:08:41] [1] "black"
INFO [2024-02-20 21:08:41] 
INFO [2024-02-20 21:08:41] $cat.fontface
INFO [2024-02-20 21:08:41] [1] "plain"
INFO [2024-02-20 21:08:41] 
INFO [2024-02-20 21:08:41] $cat.fontfamily
INFO [2024-02-20 21:08:41] [1] "serif"
INFO [2024-02-20 21:08:41] 
INFO [2024-02-20 21:08:41] $x
INFO [2024-02-20 21:08:41] $x$TF1
INFO [2024-02-20 21:08:41] [1] 3 4 5
INFO [2024-02-20 21:08:41] 
INFO [2024-02-20 21:08:41] $x$TF2
INFO [2024-02-20 21:08:41] [1] 1 2 5
INFO [2024-02-20 21:08:41] 
INFO [2024-02-20 21:08:41] $x$TF3
INFO [2024-02-20 21:08:41] [1] 1 2 5
INFO [2024-02-20 21:08:41] 
INFO [2024-02-20 21:08:41] 
INFO [2024-02-20 21:08:41] $filename
INFO [2024-02-20 21:08:41] NULL
INFO [2024-02-20 21:08:41] 
INFO [2024-02-20 21:08:41] $disable.logging
INFO [2024-02-20 21:08:41] [1] TRUE
INFO [2024-02-20 21:08:41] 
INFO [2024-02-20 21:08:41] $scaled
INFO [2024-02-20 21:08:41] [1] FALSE
INFO [2024-02-20 21:08:41] 
INFO [2024-02-20 21:08:41] $euler.d
INFO [2024-02-20 21:08:41] [1] FALSE
INFO [2024-02-20 21:08:41] 
INFO [2024-02-20 21:08:41] $cat.cex
INFO [2024-02-20 21:08:41] [1] 1
INFO [2024-02-20 21:08:41] 
INFO [2024-02-20 21:08:41] $cat.col
INFO [2024-02-20 21:08:41] [1] "black"
INFO [2024-02-20 21:08:41] 
INFO [2024-02-20 21:08:41] $cat.fontface
INFO [2024-02-20 21:08:41] [1] "plain"
INFO [2024-02-20 21:08:41] 
INFO [2024-02-20 21:08:41] $cat.fontfamily
INFO [2024-02-20 21:08:41] [1] "serif"
INFO [2024-02-20 21:08:41] 
INFO [2024-02-20 21:08:41] $x
INFO [2024-02-20 21:08:41] $x$TF1
INFO [2024-02-20 21:08:41] [1] 3 4 5
INFO [2024-02-20 21:08:41] 
INFO [2024-02-20 21:08:41] $x$TF2
INFO [2024-02-20 21:08:41] [1] 1 2 5
INFO [2024-02-20 21:08:41] 
INFO [2024-02-20 21:08:41] $x$TF3
INFO [2024-02-20 21:08:41] [1] 1 2 5
INFO [2024-02-20 21:08:41] 
INFO [2024-02-20 21:08:41] $x$TF4
INFO [2024-02-20 21:08:41] [1] 1 2 5
INFO [2024-02-20 21:08:41] 
INFO [2024-02-20 21:08:41] 
INFO [2024-02-20 21:08:41] $filename
INFO [2024-02-20 21:08:41] NULL
INFO [2024-02-20 21:08:41] 
INFO [2024-02-20 21:08:41] $disable.logging
INFO [2024-02-20 21:08:41] [1] TRUE
INFO [2024-02-20 21:08:41] 
[ FAIL 0 | WARN 4 | SKIP 6 | PASS 316 ]

══ 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 4 | SKIP 6 | PASS 316 ]
> 
> proc.time()
   user  system elapsed 
155.342   3.945 160.493 

Example timings

ChIPpeakAnno.Rcheck/ChIPpeakAnno-Ex.timings

nameusersystemelapsed
ChIPpeakAnno-package0.0010.0000.001
ExonPlusUtr.human.GRCh373.0920.2233.316
HOT.spots0.1280.0160.145
IDRfilter000
Peaks.Ste12.Replicate10.050.000.05
Peaks.Ste12.Replicate20.0080.0040.012
Peaks.Ste12.Replicate30.0130.0000.013
TSS.human.GRCh370.1770.0160.194
TSS.human.GRCh380.1440.0000.144
TSS.human.NCBI360.1050.0040.109
TSS.mouse.GRCm380.0890.0160.105
TSS.mouse.NCBIM370.0960.0000.096
TSS.rat.RGSC3.40.0800.0030.083
TSS.rat.Rnor_5.00.0680.0040.072
TSS.zebrafish.Zv80.0730.0050.077
TSS.zebrafish.Zv90.0820.0070.089
addAncestors1.0180.0731.092
addGeneIDs0.8440.0640.908
addMetadata1.0720.0841.155
annoGR000
annoPeaks3.5690.2364.665
annotatePeakInBatch13.372 1.14414.516
annotatedPeak0.060.000.06
assignChromosomeRegion0.0010.0000.001
bdp0.0010.0000.001
binOverFeature0.7850.0200.806
binOverGene0.0000.0000.001
binOverRegions0.0000.0000.001
condenseMatrixByColnames0.0100.0000.011
convert2EntrezID0.3730.0000.373
countPatternInSeqs0.1690.0040.173
cumulativePercentage000
downstreams0.0230.0000.022
egOrgMap0.0000.0000.001
enrichedGO0.0020.0000.002
enrichmentPlot0.5040.0040.507
estFragmentLength000
estLibSize000
featureAlignedDistribution0.2280.0070.234
featureAlignedExtendSignal0.0010.0000.001
featureAlignedHeatmap0.4280.0080.436
featureAlignedSignal0.1650.0240.189
findEnhancers23.598 0.53624.133
findMotifsInPromoterSeqs12.908 0.21613.133
findOverlappingPeaks0.0000.0000.001
findOverlapsOfPeaks1.6270.0041.631
genomicElementDistribution0.0010.0000.001
genomicElementUpSetR0.0000.0000.001
getAllPeakSequence0.4950.0080.502
getAnnotation0.0000.0000.001
getEnrichedGO0.0080.0000.007
getEnrichedPATH0.0010.0000.000
getGO000
getGeneSeq0.0010.0000.001
getUniqueGOidCount0.0000.0000.001
getVennCounts0.0000.0000.001
hyperGtest0.0010.0000.000
makeVennDiagram0.0020.0000.002
mergePlusMinusPeaks0.0010.0000.000
metagenePlot1.8340.0241.858
myPeakList0.0150.0000.015
oligoFrequency0.1490.0040.153
oligoSummary0.0010.0000.000
peakPermTest0.0010.0000.001
peaksNearBDP0.0000.0000.001
pie10.0050.0000.005
plotBinOverRegions000
preparePool0.0010.0000.000
reCenterPeaks0.0970.0040.101
summarizeOverlapsByBins4.9730.5095.217
summarizePatternInPeaks0.5370.0400.577
tileCount0.1730.1670.288
tileGRanges0.1000.1180.033
toGRanges0.0680.0160.084
translatePattern0.0010.0000.001
wgEncodeTfbsV30.2160.0120.228
write2FASTA0.0160.0000.016
xget0.0930.0120.105