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This page was generated on 2024-04-17 11:36:37 -0400 (Wed, 17 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4676
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4414
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4437
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: 2024-04-15 14:05:01 -0400 (Mon, 15 Apr 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 -0400 (Thu, 15 Feb 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 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 palomino4


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: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ChIPpeakAnno.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings ChIPpeakAnno_3.36.1.tar.gz
StartedAt: 2024-04-15 23:14:58 -0400 (Mon, 15 Apr 2024)
EndedAt: 2024-04-15 23:26:48 -0400 (Mon, 15 Apr 2024)
EllapsedTime: 710.8 seconds
RetCode: 0
Status:   OK  
CheckDir: ChIPpeakAnno.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ChIPpeakAnno.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings ChIPpeakAnno_3.36.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/ChIPpeakAnno.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'ChIPpeakAnno/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ChIPpeakAnno' version '3.36.1'
* 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 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 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            30.83   1.42   32.97
findMotifsInPromoterSeqs 15.75   0.36   16.38
annotatePeakInBatch      13.75   1.23   16.20
summarizeOverlapsByBins   4.07   0.05   22.35
tileCount                 1.33   0.04   21.19
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

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

Installation output

ChIPpeakAnno.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL ChIPpeakAnno
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.18-bioc/R/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 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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


Attaching package: 'IRanges'

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

    windows

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 [2024-04-15 23:26:25] $cat.cex
INFO [2024-04-15 23:26:25] [1] 1
INFO [2024-04-15 23:26:25] 
INFO [2024-04-15 23:26:25] $cat.col
INFO [2024-04-15 23:26:25] [1] "black"
INFO [2024-04-15 23:26:25] 
INFO [2024-04-15 23:26:25] $cat.fontface
INFO [2024-04-15 23:26:25] [1] "plain"
INFO [2024-04-15 23:26:25] 
INFO [2024-04-15 23:26:25] $cat.fontfamily
INFO [2024-04-15 23:26:25] [1] "serif"
INFO [2024-04-15 23:26:25] 
INFO [2024-04-15 23:26:25] $x
INFO [2024-04-15 23:26:25] $x$TF1
INFO [2024-04-15 23:26:25] [1] 3 4 5
INFO [2024-04-15 23:26:25] 
INFO [2024-04-15 23:26:25] $x$TF2
INFO [2024-04-15 23:26:25] [1] 1 2 3 4 5
INFO [2024-04-15 23:26:25] 
INFO [2024-04-15 23:26:25] 
INFO [2024-04-15 23:26:25] $filename
INFO [2024-04-15 23:26:25] NULL
INFO [2024-04-15 23:26:25] 
INFO [2024-04-15 23:26:25] $disable.logging
INFO [2024-04-15 23:26:25] [1] TRUE
INFO [2024-04-15 23:26:25] 
INFO [2024-04-15 23:26:25] $cat.cex
INFO [2024-04-15 23:26:25] [1] 1
INFO [2024-04-15 23:26:25] 
INFO [2024-04-15 23:26:25] $cat.col
INFO [2024-04-15 23:26:25] [1] "black"
INFO [2024-04-15 23:26:25] 
INFO [2024-04-15 23:26:25] $cat.fontface
INFO [2024-04-15 23:26:25] [1] "plain"
INFO [2024-04-15 23:26:25] 
INFO [2024-04-15 23:26:25] $cat.fontfamily
INFO [2024-04-15 23:26:25] [1] "serif"
INFO [2024-04-15 23:26:25] 
INFO [2024-04-15 23:26:25] $x
INFO [2024-04-15 23:26:25] $x$TF1
INFO [2024-04-15 23:26:25] [1] 3 4 5
INFO [2024-04-15 23:26:25] 
INFO [2024-04-15 23:26:25] $x$TF2
INFO [2024-04-15 23:26:25] [1] 1 2 4 5
INFO [2024-04-15 23:26:25] 
INFO [2024-04-15 23:26:25] $x$TF3
INFO [2024-04-15 23:26:25] [1] 3 4 5
INFO [2024-04-15 23:26:25] 
INFO [2024-04-15 23:26:25] $x$TF4
INFO [2024-04-15 23:26:25] [1] 1 2 4 5
INFO [2024-04-15 23:26:25] 
INFO [2024-04-15 23:26:25] 
INFO [2024-04-15 23:26:25] $filename
INFO [2024-04-15 23:26:25] NULL
INFO [2024-04-15 23:26:25] 
INFO [2024-04-15 23:26:25] $disable.logging
INFO [2024-04-15 23:26:25] [1] TRUE
INFO [2024-04-15 23:26:25] 
INFO [2024-04-15 23:26:26] $scaled
INFO [2024-04-15 23:26:26] [1] FALSE
INFO [2024-04-15 23:26:26] 
INFO [2024-04-15 23:26:26] $euler.d
INFO [2024-04-15 23:26:26] [1] FALSE
INFO [2024-04-15 23:26:26] 
INFO [2024-04-15 23:26:26] $cat.cex
INFO [2024-04-15 23:26:26] [1] 1
INFO [2024-04-15 23:26:26] 
INFO [2024-04-15 23:26:26] $cat.col
INFO [2024-04-15 23:26:26] [1] "black"
INFO [2024-04-15 23:26:26] 
INFO [2024-04-15 23:26:26] $cat.fontface
INFO [2024-04-15 23:26:26] [1] "plain"
INFO [2024-04-15 23:26:26] 
INFO [2024-04-15 23:26:26] $cat.fontfamily
INFO [2024-04-15 23:26:26] [1] "serif"
INFO [2024-04-15 23:26:26] 
INFO [2024-04-15 23:26:26] $x
INFO [2024-04-15 23:26:26] $x$TF1
INFO [2024-04-15 23:26:26] [1] 1 2 3
INFO [2024-04-15 23:26:26] 
INFO [2024-04-15 23:26:26] $x$TF2
INFO [2024-04-15 23:26:26] [1] 1 2 3
INFO [2024-04-15 23:26:26] 
INFO [2024-04-15 23:26:26] 
INFO [2024-04-15 23:26:26] $filename
INFO [2024-04-15 23:26:26] NULL
INFO [2024-04-15 23:26:26] 
INFO [2024-04-15 23:26:26] $disable.logging
INFO [2024-04-15 23:26:26] [1] TRUE
INFO [2024-04-15 23:26:26] 
INFO [2024-04-15 23:26:26] $scaled
INFO [2024-04-15 23:26:26] [1] FALSE
INFO [2024-04-15 23:26:26] 
INFO [2024-04-15 23:26:26] $euler.d
INFO [2024-04-15 23:26:26] [1] FALSE
INFO [2024-04-15 23:26:26] 
INFO [2024-04-15 23:26:26] $cat.cex
INFO [2024-04-15 23:26:26] [1] 1
INFO [2024-04-15 23:26:26] 
INFO [2024-04-15 23:26:26] $cat.col
INFO [2024-04-15 23:26:26] [1] "black"
INFO [2024-04-15 23:26:26] 
INFO [2024-04-15 23:26:26] $cat.fontface
INFO [2024-04-15 23:26:26] [1] "plain"
INFO [2024-04-15 23:26:26] 
INFO [2024-04-15 23:26:26] $cat.fontfamily
INFO [2024-04-15 23:26:26] [1] "serif"
INFO [2024-04-15 23:26:26] 
INFO [2024-04-15 23:26:26] $x
INFO [2024-04-15 23:26:26] $x$TF1
INFO [2024-04-15 23:26:26] [1] 4 5 6
INFO [2024-04-15 23:26:26] 
INFO [2024-04-15 23:26:26] $x$TF2
INFO [2024-04-15 23:26:26] [1] 1 2 3
INFO [2024-04-15 23:26:26] 
INFO [2024-04-15 23:26:26] 
INFO [2024-04-15 23:26:26] $filename
INFO [2024-04-15 23:26:26] NULL
INFO [2024-04-15 23:26:26] 
INFO [2024-04-15 23:26:26] $disable.logging
INFO [2024-04-15 23:26:26] [1] TRUE
INFO [2024-04-15 23:26:26] 
INFO [2024-04-15 23:26:26] $scaled
INFO [2024-04-15 23:26:26] [1] FALSE
INFO [2024-04-15 23:26:26] 
INFO [2024-04-15 23:26:26] $euler.d
INFO [2024-04-15 23:26:26] [1] FALSE
INFO [2024-04-15 23:26:26] 
INFO [2024-04-15 23:26:26] $cat.cex
INFO [2024-04-15 23:26:26] [1] 1
INFO [2024-04-15 23:26:26] 
INFO [2024-04-15 23:26:26] $cat.col
INFO [2024-04-15 23:26:26] [1] "black"
INFO [2024-04-15 23:26:26] 
INFO [2024-04-15 23:26:26] $cat.fontface
INFO [2024-04-15 23:26:26] [1] "plain"
INFO [2024-04-15 23:26:26] 
INFO [2024-04-15 23:26:26] $cat.fontfamily
INFO [2024-04-15 23:26:26] [1] "serif"
INFO [2024-04-15 23:26:26] 
INFO [2024-04-15 23:26:26] $x
INFO [2024-04-15 23:26:26] $x$TF1
INFO [2024-04-15 23:26:26] [1] 4 5 6
INFO [2024-04-15 23:26:26] 
INFO [2024-04-15 23:26:26] $x$TF2
INFO [2024-04-15 23:26:26] [1] 1 2 3
INFO [2024-04-15 23:26:26] 
INFO [2024-04-15 23:26:26] 
INFO [2024-04-15 23:26:26] $filename
INFO [2024-04-15 23:26:26] NULL
INFO [2024-04-15 23:26:26] 
INFO [2024-04-15 23:26:26] $disable.logging
INFO [2024-04-15 23:26:26] [1] TRUE
INFO [2024-04-15 23:26:26] 
INFO [2024-04-15 23:26:27] $scaled
INFO [2024-04-15 23:26:27] [1] FALSE
INFO [2024-04-15 23:26:27] 
INFO [2024-04-15 23:26:27] $euler.d
INFO [2024-04-15 23:26:27] [1] FALSE
INFO [2024-04-15 23:26:27] 
INFO [2024-04-15 23:26:27] $cat.cex
INFO [2024-04-15 23:26:27] [1] 1
INFO [2024-04-15 23:26:27] 
INFO [2024-04-15 23:26:27] $cat.col
INFO [2024-04-15 23:26:27] [1] "black"
INFO [2024-04-15 23:26:27] 
INFO [2024-04-15 23:26:27] $cat.fontface
INFO [2024-04-15 23:26:27] [1] "plain"
INFO [2024-04-15 23:26:27] 
INFO [2024-04-15 23:26:27] $cat.fontfamily
INFO [2024-04-15 23:26:27] [1] "serif"
INFO [2024-04-15 23:26:27] 
INFO [2024-04-15 23:26:27] $x
INFO [2024-04-15 23:26:27] $x$TF1
INFO [2024-04-15 23:26:27] [1] 4 5 6
INFO [2024-04-15 23:26:27] 
INFO [2024-04-15 23:26:27] $x$TF2
INFO [2024-04-15 23:26:27] [1] 1 2 3
INFO [2024-04-15 23:26:27] 
INFO [2024-04-15 23:26:27] $x$TF3
INFO [2024-04-15 23:26:27] [1] 2 3 6
INFO [2024-04-15 23:26:27] 
INFO [2024-04-15 23:26:27] 
INFO [2024-04-15 23:26:27] $filename
INFO [2024-04-15 23:26:27] NULL
INFO [2024-04-15 23:26:27] 
INFO [2024-04-15 23:26:27] $disable.logging
INFO [2024-04-15 23:26:27] [1] TRUE
INFO [2024-04-15 23:26:27] 
INFO [2024-04-15 23:26:27] $scaled
INFO [2024-04-15 23:26:27] [1] FALSE
INFO [2024-04-15 23:26:27] 
INFO [2024-04-15 23:26:27] $euler.d
INFO [2024-04-15 23:26:27] [1] FALSE
INFO [2024-04-15 23:26:27] 
INFO [2024-04-15 23:26:27] $cat.cex
INFO [2024-04-15 23:26:27] [1] 1
INFO [2024-04-15 23:26:27] 
INFO [2024-04-15 23:26:27] $cat.col
INFO [2024-04-15 23:26:27] [1] "black"
INFO [2024-04-15 23:26:27] 
INFO [2024-04-15 23:26:27] $cat.fontface
INFO [2024-04-15 23:26:27] [1] "plain"
INFO [2024-04-15 23:26:27] 
INFO [2024-04-15 23:26:27] $cat.fontfamily
INFO [2024-04-15 23:26:27] [1] "serif"
INFO [2024-04-15 23:26:27] 
INFO [2024-04-15 23:26:27] $x
INFO [2024-04-15 23:26:27] $x$TF1
INFO [2024-04-15 23:26:27] [1] 3 4 5
INFO [2024-04-15 23:26:27] 
INFO [2024-04-15 23:26:27] $x$TF2
INFO [2024-04-15 23:26:27] [1] 1 2 5
INFO [2024-04-15 23:26:27] 
INFO [2024-04-15 23:26:27] $x$TF3
INFO [2024-04-15 23:26:27] [1] 1 2 5
INFO [2024-04-15 23:26:27] 
INFO [2024-04-15 23:26:27] 
INFO [2024-04-15 23:26:27] $filename
INFO [2024-04-15 23:26:27] NULL
INFO [2024-04-15 23:26:27] 
INFO [2024-04-15 23:26:27] $disable.logging
INFO [2024-04-15 23:26:27] [1] TRUE
INFO [2024-04-15 23:26:27] 
INFO [2024-04-15 23:26:27] $scaled
INFO [2024-04-15 23:26:27] [1] FALSE
INFO [2024-04-15 23:26:27] 
INFO [2024-04-15 23:26:27] $euler.d
INFO [2024-04-15 23:26:27] [1] FALSE
INFO [2024-04-15 23:26:27] 
INFO [2024-04-15 23:26:27] $cat.cex
INFO [2024-04-15 23:26:27] [1] 1
INFO [2024-04-15 23:26:27] 
INFO [2024-04-15 23:26:27] $cat.col
INFO [2024-04-15 23:26:27] [1] "black"
INFO [2024-04-15 23:26:27] 
INFO [2024-04-15 23:26:27] $cat.fontface
INFO [2024-04-15 23:26:27] [1] "plain"
INFO [2024-04-15 23:26:27] 
INFO [2024-04-15 23:26:27] $cat.fontfamily
INFO [2024-04-15 23:26:27] [1] "serif"
INFO [2024-04-15 23:26:27] 
INFO [2024-04-15 23:26:27] $x
INFO [2024-04-15 23:26:27] $x$TF1
INFO [2024-04-15 23:26:27] [1] 3 4 5
INFO [2024-04-15 23:26:27] 
INFO [2024-04-15 23:26:27] $x$TF2
INFO [2024-04-15 23:26:27] [1] 1 2 5
INFO [2024-04-15 23:26:27] 
INFO [2024-04-15 23:26:27] $x$TF3
INFO [2024-04-15 23:26:27] [1] 1 2 5
INFO [2024-04-15 23:26:27] 
INFO [2024-04-15 23:26:27] $x$TF4
INFO [2024-04-15 23:26:27] [1] 1 2 5
INFO [2024-04-15 23:26:27] 
INFO [2024-04-15 23:26:27] 
INFO [2024-04-15 23:26:27] $filename
INFO [2024-04-15 23:26:27] NULL
INFO [2024-04-15 23:26:27] 
INFO [2024-04-15 23:26:27] $disable.logging
INFO [2024-04-15 23:26:27] [1] TRUE
INFO [2024-04-15 23:26:27] 
[ 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 
 197.40    9.28  216.50

Example timings

ChIPpeakAnno.Rcheck/ChIPpeakAnno-Ex.timings

nameusersystemelapsed
ChIPpeakAnno-package000
ExonPlusUtr.human.GRCh373.800.043.84
HOT.spots0.110.000.11
IDRfilter000
Peaks.Ste12.Replicate10.040.000.05
Peaks.Ste12.Replicate20.020.000.02
Peaks.Ste12.Replicate30.030.000.03
TSS.human.GRCh370.190.030.22
TSS.human.GRCh380.120.030.15
TSS.human.NCBI360.100.020.11
TSS.mouse.GRCm380.110.010.13
TSS.mouse.NCBIM370.070.020.09
TSS.rat.RGSC3.40.080.000.07
TSS.rat.Rnor_5.00.060.000.07
TSS.zebrafish.Zv80.070.010.07
TSS.zebrafish.Zv90.090.000.10
addAncestors0.940.050.98
addGeneIDs2.951.474.42
addMetadata1.800.091.89
annoGR000
annoPeaks3.400.454.39
annotatePeakInBatch13.75 1.2316.20
annotatedPeak0.050.000.05
assignChromosomeRegion0.010.000.01
bdp000
binOverFeature0.830.030.97
binOverGene000
binOverRegions000
condenseMatrixByColnames0.020.000.02
convert2EntrezID0.390.000.39
countPatternInSeqs0.150.040.18
cumulativePercentage000
downstreams0.030.000.04
egOrgMap000
enrichedGO0.000.010.01
enrichmentPlot0.790.030.83
estFragmentLength000
estLibSize0.000.020.02
featureAlignedDistribution0.320.000.32
featureAlignedExtendSignal000
featureAlignedHeatmap0.320.000.32
featureAlignedSignal0.150.060.21
findEnhancers30.83 1.4232.97
findMotifsInPromoterSeqs15.75 0.3616.38
findOverlappingPeaks000
findOverlapsOfPeaks2.110.052.16
genomicElementDistribution000
genomicElementUpSetR0.010.000.02
getAllPeakSequence0.830.080.96
getAnnotation000
getEnrichedGO0.020.010.04
getEnrichedPATH000
getGO000
getGeneSeq0.010.000.01
getUniqueGOidCount000
getVennCounts000
hyperGtest000
makeVennDiagram000
mergePlusMinusPeaks000
metagenePlot2.680.082.81
myPeakList0.020.000.02
oligoFrequency0.230.000.23
oligoSummary000
peakPermTest000
peaksNearBDP000
pie10.020.000.01
plotBinOverRegions000
preparePool000
reCenterPeaks0.030.000.03
summarizeOverlapsByBins 4.07 0.0522.35
summarizePatternInPeaks0.520.000.51
tileCount 1.33 0.0421.19
tileGRanges0.050.000.05
toGRanges0.100.000.11
translatePattern000
wgEncodeTfbsV30.190.000.18
write2FASTA0.020.000.02
xget0.090.020.11