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This page was generated on 2024-02-05 12:53:32 -0500 (Mon, 05 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4624
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4366
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4393
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4300
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 332/2237HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPpeakAnno 3.37.4  (landing page)
Jianhong Ou
Snapshot Date: 2024-02-04 14:00:13 -0500 (Sun, 04 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
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for ChIPpeakAnno on merida1


To the developers/maintainers of the ChIPpeakAnno package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ChIPpeakAnno.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: ChIPpeakAnno
Version: 3.37.4
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ChIPpeakAnno_3.37.4.tar.gz
StartedAt: 2024-02-05 00:24:51 -0500 (Mon, 05 Feb 2024)
EndedAt: 2024-02-05 00:45:51 -0500 (Mon, 05 Feb 2024)
EllapsedTime: 1260.2 seconds
RetCode: 0
Status:   OK  
CheckDir: ChIPpeakAnno.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ChIPpeakAnno_3.37.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/ChIPpeakAnno.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChIPpeakAnno/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChIPpeakAnno’ version ‘3.37.4’
* 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 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 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 ... 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            54.785  1.056  56.928
findMotifsInPromoterSeqs 29.834  0.744  32.665
annotatePeakInBatch      26.122  1.079  27.663
summarizeOverlapsByBins   5.987  0.785   6.744
annoPeaks                 5.712  0.520   8.164
addGeneIDs                3.769  1.190   5.798
ExonPlusUtr.human.GRCh37  4.532  0.168   5.342
metagenePlot              3.693  0.117   7.700
findOverlapsOfPeaks       3.482  0.073   5.234
getAllPeakSequence        0.888  0.042   6.102
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/ChIPpeakAnno.Rcheck/00check.log’
for details.



Installation output

ChIPpeakAnno.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ChIPpeakAnno
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘ChIPpeakAnno’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ChIPpeakAnno)

Tests output

ChIPpeakAnno.Rcheck/tests/runTests.Rout


R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> require("ChIPpeakAnno") || stop("unable to load Package:ChIPpeakAnno")
Loading required package: ChIPpeakAnno
Loading required package: IRanges
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, 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 [2024-02-05 00:45:06] $cat.cex
INFO [2024-02-05 00:45:06] [1] 1
INFO [2024-02-05 00:45:06] 
INFO [2024-02-05 00:45:06] $cat.col
INFO [2024-02-05 00:45:06] [1] "black"
INFO [2024-02-05 00:45:06] 
INFO [2024-02-05 00:45:06] $cat.fontface
INFO [2024-02-05 00:45:06] [1] "plain"
INFO [2024-02-05 00:45:06] 
INFO [2024-02-05 00:45:06] $cat.fontfamily
INFO [2024-02-05 00:45:06] [1] "serif"
INFO [2024-02-05 00:45:06] 
INFO [2024-02-05 00:45:06] $x
INFO [2024-02-05 00:45:06] $x$TF1
INFO [2024-02-05 00:45:06] [1] 3 4 5
INFO [2024-02-05 00:45:06] 
INFO [2024-02-05 00:45:06] $x$TF2
INFO [2024-02-05 00:45:06] [1] 1 2 3 4 5
INFO [2024-02-05 00:45:06] 
INFO [2024-02-05 00:45:06] 
INFO [2024-02-05 00:45:06] $disable.logging
INFO [2024-02-05 00:45:06] [1] TRUE
INFO [2024-02-05 00:45:06] 
INFO [2024-02-05 00:45:06] $filename
INFO [2024-02-05 00:45:06] NULL
INFO [2024-02-05 00:45:06] 
INFO [2024-02-05 00:45:06] $cat.cex
INFO [2024-02-05 00:45:06] [1] 1
INFO [2024-02-05 00:45:06] 
INFO [2024-02-05 00:45:06] $cat.col
INFO [2024-02-05 00:45:06] [1] "black"
INFO [2024-02-05 00:45:06] 
INFO [2024-02-05 00:45:06] $cat.fontface
INFO [2024-02-05 00:45:06] [1] "plain"
INFO [2024-02-05 00:45:06] 
INFO [2024-02-05 00:45:06] $cat.fontfamily
INFO [2024-02-05 00:45:06] [1] "serif"
INFO [2024-02-05 00:45:06] 
INFO [2024-02-05 00:45:06] $x
INFO [2024-02-05 00:45:06] $x$TF1
INFO [2024-02-05 00:45:06] [1] 3 4 5
INFO [2024-02-05 00:45:06] 
INFO [2024-02-05 00:45:06] $x$TF2
INFO [2024-02-05 00:45:06] [1] 1 2 4 5
INFO [2024-02-05 00:45:06] 
INFO [2024-02-05 00:45:06] $x$TF3
INFO [2024-02-05 00:45:06] [1] 3 4 5
INFO [2024-02-05 00:45:06] 
INFO [2024-02-05 00:45:06] $x$TF4
INFO [2024-02-05 00:45:06] [1] 1 2 4 5
INFO [2024-02-05 00:45:06] 
INFO [2024-02-05 00:45:06] 
INFO [2024-02-05 00:45:06] $disable.logging
INFO [2024-02-05 00:45:06] [1] TRUE
INFO [2024-02-05 00:45:06] 
INFO [2024-02-05 00:45:06] $filename
INFO [2024-02-05 00:45:06] NULL
INFO [2024-02-05 00:45:06] 
INFO [2024-02-05 00:45:07] $scaled
INFO [2024-02-05 00:45:07] [1] FALSE
INFO [2024-02-05 00:45:07] 
INFO [2024-02-05 00:45:07] $euler.d
INFO [2024-02-05 00:45:07] [1] FALSE
INFO [2024-02-05 00:45:07] 
INFO [2024-02-05 00:45:07] $cat.cex
INFO [2024-02-05 00:45:07] [1] 1
INFO [2024-02-05 00:45:07] 
INFO [2024-02-05 00:45:07] $cat.col
INFO [2024-02-05 00:45:07] [1] "black"
INFO [2024-02-05 00:45:07] 
INFO [2024-02-05 00:45:07] $cat.fontface
INFO [2024-02-05 00:45:07] [1] "plain"
INFO [2024-02-05 00:45:07] 
INFO [2024-02-05 00:45:07] $cat.fontfamily
INFO [2024-02-05 00:45:07] [1] "serif"
INFO [2024-02-05 00:45:07] 
INFO [2024-02-05 00:45:07] $x
INFO [2024-02-05 00:45:07] $x$TF1
INFO [2024-02-05 00:45:07] [1] 1 2 3
INFO [2024-02-05 00:45:07] 
INFO [2024-02-05 00:45:07] $x$TF2
INFO [2024-02-05 00:45:07] [1] 1 2 3
INFO [2024-02-05 00:45:07] 
INFO [2024-02-05 00:45:07] 
INFO [2024-02-05 00:45:07] $disable.logging
INFO [2024-02-05 00:45:07] [1] TRUE
INFO [2024-02-05 00:45:07] 
INFO [2024-02-05 00:45:07] $filename
INFO [2024-02-05 00:45:07] NULL
INFO [2024-02-05 00:45:07] 
INFO [2024-02-05 00:45:08] $scaled
INFO [2024-02-05 00:45:08] [1] FALSE
INFO [2024-02-05 00:45:08] 
INFO [2024-02-05 00:45:08] $euler.d
INFO [2024-02-05 00:45:08] [1] FALSE
INFO [2024-02-05 00:45:08] 
INFO [2024-02-05 00:45:08] $cat.cex
INFO [2024-02-05 00:45:08] [1] 1
INFO [2024-02-05 00:45:08] 
INFO [2024-02-05 00:45:08] $cat.col
INFO [2024-02-05 00:45:08] [1] "black"
INFO [2024-02-05 00:45:08] 
INFO [2024-02-05 00:45:08] $cat.fontface
INFO [2024-02-05 00:45:08] [1] "plain"
INFO [2024-02-05 00:45:08] 
INFO [2024-02-05 00:45:08] $cat.fontfamily
INFO [2024-02-05 00:45:08] [1] "serif"
INFO [2024-02-05 00:45:08] 
INFO [2024-02-05 00:45:08] $x
INFO [2024-02-05 00:45:08] $x$TF1
INFO [2024-02-05 00:45:08] [1] 4 5 6
INFO [2024-02-05 00:45:08] 
INFO [2024-02-05 00:45:08] $x$TF2
INFO [2024-02-05 00:45:08] [1] 1 2 3
INFO [2024-02-05 00:45:08] 
INFO [2024-02-05 00:45:08] 
INFO [2024-02-05 00:45:08] $disable.logging
INFO [2024-02-05 00:45:08] [1] TRUE
INFO [2024-02-05 00:45:08] 
INFO [2024-02-05 00:45:08] $filename
INFO [2024-02-05 00:45:08] NULL
INFO [2024-02-05 00:45:08] 
INFO [2024-02-05 00:45:08] $scaled
INFO [2024-02-05 00:45:08] [1] FALSE
INFO [2024-02-05 00:45:08] 
INFO [2024-02-05 00:45:08] $euler.d
INFO [2024-02-05 00:45:08] [1] FALSE
INFO [2024-02-05 00:45:08] 
INFO [2024-02-05 00:45:08] $cat.cex
INFO [2024-02-05 00:45:08] [1] 1
INFO [2024-02-05 00:45:08] 
INFO [2024-02-05 00:45:08] $cat.col
INFO [2024-02-05 00:45:08] [1] "black"
INFO [2024-02-05 00:45:08] 
INFO [2024-02-05 00:45:08] $cat.fontface
INFO [2024-02-05 00:45:08] [1] "plain"
INFO [2024-02-05 00:45:08] 
INFO [2024-02-05 00:45:08] $cat.fontfamily
INFO [2024-02-05 00:45:08] [1] "serif"
INFO [2024-02-05 00:45:08] 
INFO [2024-02-05 00:45:08] $x
INFO [2024-02-05 00:45:08] $x$TF1
INFO [2024-02-05 00:45:08] [1] 4 5 6
INFO [2024-02-05 00:45:08] 
INFO [2024-02-05 00:45:08] $x$TF2
INFO [2024-02-05 00:45:08] [1] 1 2 3
INFO [2024-02-05 00:45:08] 
INFO [2024-02-05 00:45:08] 
INFO [2024-02-05 00:45:08] $disable.logging
INFO [2024-02-05 00:45:08] [1] TRUE
INFO [2024-02-05 00:45:08] 
INFO [2024-02-05 00:45:08] $filename
INFO [2024-02-05 00:45:08] NULL
INFO [2024-02-05 00:45:08] 
INFO [2024-02-05 00:45:09] $scaled
INFO [2024-02-05 00:45:09] [1] FALSE
INFO [2024-02-05 00:45:09] 
INFO [2024-02-05 00:45:09] $euler.d
INFO [2024-02-05 00:45:09] [1] FALSE
INFO [2024-02-05 00:45:09] 
INFO [2024-02-05 00:45:09] $cat.cex
INFO [2024-02-05 00:45:09] [1] 1
INFO [2024-02-05 00:45:09] 
INFO [2024-02-05 00:45:09] $cat.col
INFO [2024-02-05 00:45:09] [1] "black"
INFO [2024-02-05 00:45:09] 
INFO [2024-02-05 00:45:09] $cat.fontface
INFO [2024-02-05 00:45:09] [1] "plain"
INFO [2024-02-05 00:45:09] 
INFO [2024-02-05 00:45:09] $cat.fontfamily
INFO [2024-02-05 00:45:09] [1] "serif"
INFO [2024-02-05 00:45:09] 
INFO [2024-02-05 00:45:09] $x
INFO [2024-02-05 00:45:09] $x$TF1
INFO [2024-02-05 00:45:09] [1] 4 5 6
INFO [2024-02-05 00:45:09] 
INFO [2024-02-05 00:45:09] $x$TF2
INFO [2024-02-05 00:45:09] [1] 1 2 3
INFO [2024-02-05 00:45:09] 
INFO [2024-02-05 00:45:09] $x$TF3
INFO [2024-02-05 00:45:09] [1] 2 3 6
INFO [2024-02-05 00:45:09] 
INFO [2024-02-05 00:45:09] 
INFO [2024-02-05 00:45:09] $disable.logging
INFO [2024-02-05 00:45:09] [1] TRUE
INFO [2024-02-05 00:45:09] 
INFO [2024-02-05 00:45:09] $filename
INFO [2024-02-05 00:45:09] NULL
INFO [2024-02-05 00:45:09] 
INFO [2024-02-05 00:45:10] $scaled
INFO [2024-02-05 00:45:10] [1] FALSE
INFO [2024-02-05 00:45:10] 
INFO [2024-02-05 00:45:10] $euler.d
INFO [2024-02-05 00:45:10] [1] FALSE
INFO [2024-02-05 00:45:10] 
INFO [2024-02-05 00:45:10] $cat.cex
INFO [2024-02-05 00:45:10] [1] 1
INFO [2024-02-05 00:45:10] 
INFO [2024-02-05 00:45:10] $cat.col
INFO [2024-02-05 00:45:10] [1] "black"
INFO [2024-02-05 00:45:10] 
INFO [2024-02-05 00:45:10] $cat.fontface
INFO [2024-02-05 00:45:10] [1] "plain"
INFO [2024-02-05 00:45:10] 
INFO [2024-02-05 00:45:10] $cat.fontfamily
INFO [2024-02-05 00:45:10] [1] "serif"
INFO [2024-02-05 00:45:10] 
INFO [2024-02-05 00:45:10] $x
INFO [2024-02-05 00:45:10] $x$TF1
INFO [2024-02-05 00:45:10] [1] 3 4 5
INFO [2024-02-05 00:45:10] 
INFO [2024-02-05 00:45:10] $x$TF2
INFO [2024-02-05 00:45:10] [1] 1 2 5
INFO [2024-02-05 00:45:10] 
INFO [2024-02-05 00:45:10] $x$TF3
INFO [2024-02-05 00:45:10] [1] 1 2 5
INFO [2024-02-05 00:45:10] 
INFO [2024-02-05 00:45:10] 
INFO [2024-02-05 00:45:10] $disable.logging
INFO [2024-02-05 00:45:10] [1] TRUE
INFO [2024-02-05 00:45:10] 
INFO [2024-02-05 00:45:10] $filename
INFO [2024-02-05 00:45:10] NULL
INFO [2024-02-05 00:45:10] 
INFO [2024-02-05 00:45:10] $scaled
INFO [2024-02-05 00:45:10] [1] FALSE
INFO [2024-02-05 00:45:10] 
INFO [2024-02-05 00:45:10] $euler.d
INFO [2024-02-05 00:45:10] [1] FALSE
INFO [2024-02-05 00:45:10] 
INFO [2024-02-05 00:45:10] $cat.cex
INFO [2024-02-05 00:45:10] [1] 1
INFO [2024-02-05 00:45:10] 
INFO [2024-02-05 00:45:10] $cat.col
INFO [2024-02-05 00:45:10] [1] "black"
INFO [2024-02-05 00:45:10] 
INFO [2024-02-05 00:45:10] $cat.fontface
INFO [2024-02-05 00:45:10] [1] "plain"
INFO [2024-02-05 00:45:10] 
INFO [2024-02-05 00:45:10] $cat.fontfamily
INFO [2024-02-05 00:45:10] [1] "serif"
INFO [2024-02-05 00:45:10] 
INFO [2024-02-05 00:45:10] $x
INFO [2024-02-05 00:45:10] $x$TF1
INFO [2024-02-05 00:45:10] [1] 3 4 5
INFO [2024-02-05 00:45:10] 
INFO [2024-02-05 00:45:10] $x$TF2
INFO [2024-02-05 00:45:10] [1] 1 2 5
INFO [2024-02-05 00:45:10] 
INFO [2024-02-05 00:45:10] $x$TF3
INFO [2024-02-05 00:45:10] [1] 1 2 5
INFO [2024-02-05 00:45:10] 
INFO [2024-02-05 00:45:10] $x$TF4
INFO [2024-02-05 00:45:10] [1] 1 2 5
INFO [2024-02-05 00:45:10] 
INFO [2024-02-05 00:45:10] 
INFO [2024-02-05 00:45:10] $disable.logging
INFO [2024-02-05 00:45:10] [1] TRUE
INFO [2024-02-05 00:45:10] 
INFO [2024-02-05 00:45:10] $filename
INFO [2024-02-05 00:45:10] NULL
INFO [2024-02-05 00:45:10] 
[ 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 
362.894   8.988 404.607 

Example timings

ChIPpeakAnno.Rcheck/ChIPpeakAnno-Ex.timings

nameusersystemelapsed
ChIPpeakAnno-package0.0000.0010.002
ExonPlusUtr.human.GRCh374.5320.1685.342
HOT.spots0.2030.0210.262
IDRfilter0.0020.0010.004
Peaks.Ste12.Replicate10.1010.0060.118
Peaks.Ste12.Replicate20.0260.0030.031
Peaks.Ste12.Replicate30.0250.0050.035
TSS.human.GRCh370.2630.0330.331
TSS.human.GRCh380.2100.0230.271
TSS.human.NCBI360.1550.0190.195
TSS.mouse.GRCm380.1440.0180.185
TSS.mouse.NCBIM370.1320.0130.163
TSS.rat.RGSC3.40.1100.0130.142
TSS.rat.Rnor_5.00.0960.0120.124
TSS.zebrafish.Zv80.1000.0090.125
TSS.zebrafish.Zv90.1210.0130.149
addAncestors2.3860.1192.611
addGeneIDs3.7691.1905.798
addMetadata2.7990.2793.505
annoGR0.0010.0000.002
annoPeaks5.7120.5208.164
annotatePeakInBatch26.122 1.07927.663
annotatedPeak0.0920.0080.100
assignChromosomeRegion0.0030.0010.004
bdp0.0010.0010.002
binOverFeature1.5980.0471.658
binOverGene0.0010.0010.002
binOverRegions0.0020.0010.002
condenseMatrixByColnames0.0220.0010.024
convert2EntrezID0.6870.0100.712
countPatternInSeqs0.2920.0090.306
cumulativePercentage0.0000.0000.001
downstreams0.0520.0010.053
egOrgMap0.0010.0000.001
enrichedGO0.0030.0040.007
enrichmentPlot1.0820.0221.118
estFragmentLength0.0010.0000.002
estLibSize0.0010.0010.002
featureAlignedDistribution0.6050.0090.621
featureAlignedExtendSignal0.0040.0020.005
featureAlignedHeatmap0.6860.0050.694
featureAlignedSignal0.4230.1410.570
findEnhancers54.785 1.05656.928
findMotifsInPromoterSeqs29.834 0.74432.665
findOverlappingPeaks0.0020.0020.004
findOverlapsOfPeaks3.4820.0735.234
genomicElementDistribution0.0030.0030.008
genomicElementUpSetR0.0010.0010.004
getAllPeakSequence0.8880.0426.102
getAnnotation0.0030.0030.009
getEnrichedGO0.0210.0220.048
getEnrichedPATH0.0010.0020.007
getGO0.0010.0010.004
getGeneSeq0.0030.0040.009
getUniqueGOidCount0.0020.0010.003
getVennCounts0.0020.0010.003
hyperGtest0.0020.0020.004
makeVennDiagram0.0060.0020.012
mergePlusMinusPeaks0.0020.0010.002
metagenePlot3.6930.1177.700
myPeakList0.0200.0040.025
oligoFrequency0.1680.0180.210
oligoSummary0.0020.0010.003
peakPermTest0.0020.0010.004
peaks10.0160.0060.022
peaks20.0160.0050.022
peaks30.0140.0040.019
peaksNearBDP0.0020.0010.002
pie10.0080.0020.412
plotBinOverRegions0.0020.0010.002
preparePool0.0010.0010.003
reCenterPeaks0.0520.0010.058
summarizeOverlapsByBins5.9870.7856.744
summarizePatternInPeaks3.5100.5154.743
tileCount0.7390.5430.816
tileGRanges0.0830.0260.112
toGRanges0.1980.0320.235
translatePattern0.0010.0010.002
wgEncodeTfbsV30.3380.0250.375
write2FASTA0.0330.0060.041
xget0.1740.0180.197