Multiple platform build/check report for BioC 3.20 - CHECK results for ChIPpeakAnno on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4769
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4504
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4527
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4480
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4416
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*

CHECK results for ChIPpeakAnno on nebbiolo2

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

raw results

Summary

Package: ChIPpeakAnno

Version: 3.40.0

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

StartedAt: 2025-03-03 20:46:36 -0500 (Mon, 03 Mar 2025)

EndedAt: 2025-03-03 20:56:50 -0500 (Mon, 03 Mar 2025)

EllapsedTime: 613.7 seconds

RetCode: 1

Status: ERROR

CheckDir: ChIPpeakAnno.Rcheck

Warnings: NA

Command output

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


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/ChIPpeakAnno.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘ChIPpeakAnno/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChIPpeakAnno’ version ‘3.40.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ChIPpeakAnno’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 21.1Mb
  sub-directories of 1Mb or more:
    R         1.0Mb
    data     12.6Mb
    extdata   7.2Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
findEnhancers            22.002  0.696  22.698
annotatePeakInBatch      12.050  1.144  13.195
findMotifsInPromoterSeqs 12.855  0.322  13.197
summarizeOverlapsByBins   5.647  0.603   5.954
* 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 ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘ChIPpeakAnno.Rmd’ using rmarkdown

Quitting from lines 117-127 [unnamed-chunk-5] (ChIPpeakAnno.Rmd)
Error: processing vignette 'ChIPpeakAnno.Rmd' failed with diagnostics:
Your query has been redirected to http://status.ensembl.org indicating this Ensembl service is currently unavailable.
Look at ?useEnsembl for details on how to try a mirror site.
--- failed re-building ‘ChIPpeakAnno.Rmd’

SUMMARY: processing the following file failed:
  ‘ChIPpeakAnno.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

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

Installation output

ChIPpeakAnno.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘ChIPpeakAnno’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ChIPpeakAnno)

Tests output

ChIPpeakAnno.Rcheck/tests/runTests.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
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, saveRDS, setdiff, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    findMatches

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

    I, expand.grid, unname

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
[1] TRUE
> require("BSgenome.Drerio.UCSC.danRer7") || stop("unable to load Package:BSgenome.Drerio.UCSC.danRer7")
Loading required package: BSgenome.Drerio.UCSC.danRer7
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: BiocIO
Loading required package: rtracklayer

Attaching package: 'rtracklayer'

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

    FileForFormat

[1] TRUE
> require("BSgenome.Hsapiens.UCSC.hg19") || stop("unable to load Package:BSgenome.Hsapiens.UCSC.hg19")
Loading required package: BSgenome.Hsapiens.UCSC.hg19
[1] TRUE
> require("org.Hs.eg.db") || stop("unable to load Package:org.Hs.eg.db")
Loading required package: org.Hs.eg.db
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


[1] TRUE
> require("org.Ce.eg.db") || stop("unable to load Package:org.Ce.eg.db")
Loading required package: org.Ce.eg.db

[1] TRUE
> require("BSgenome.Celegans.UCSC.ce10") || stop("unable to load Package:BSgenome.Celegans.UCSC.ce10")
Loading required package: BSgenome.Celegans.UCSC.ce10
[1] TRUE
> require("EnsDb.Hsapiens.v79") || stop("unable to load Package:EnsDb.Hsapiens.v79")
Loading required package: EnsDb.Hsapiens.v79
Loading required package: ensembldb
Loading required package: GenomicFeatures
Loading required package: AnnotationFilter

Attaching package: 'ensembldb'

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

    filter

[1] TRUE
> require("TxDb.Hsapiens.UCSC.hg38.knownGene") || stop("unable to load TxDb.Hsapiens.UCSC.hg38.knownGene")
Loading required package: TxDb.Hsapiens.UCSC.hg38.knownGene
[1] TRUE
> require("biomaRt") || stop("unable to load biomaRt")
Loading required package: biomaRt
[1] TRUE
> require("reactome.db") || stop("unable to load reactome.db")
Loading required package: reactome.db
[1] TRUE
> require("testthat") || stop("unable to load testthat")
Loading required package: testthat

Attaching package: 'testthat'

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

    not

[1] TRUE
> test_check("ChIPpeakAnno")
INFO [2025-03-03 20:56:03] $cat.cex
INFO [2025-03-03 20:56:03] [1] 1
INFO [2025-03-03 20:56:03] 
INFO [2025-03-03 20:56:03] $cat.col
INFO [2025-03-03 20:56:03] [1] "black"
INFO [2025-03-03 20:56:03] 
INFO [2025-03-03 20:56:03] $cat.fontface
INFO [2025-03-03 20:56:03] [1] "plain"
INFO [2025-03-03 20:56:03] 
INFO [2025-03-03 20:56:03] $cat.fontfamily
INFO [2025-03-03 20:56:03] [1] "serif"
INFO [2025-03-03 20:56:03] 
INFO [2025-03-03 20:56:03] $x
INFO [2025-03-03 20:56:03] $x$TF1
INFO [2025-03-03 20:56:03] [1] 3 4 5
INFO [2025-03-03 20:56:03] 
INFO [2025-03-03 20:56:03] $x$TF2
INFO [2025-03-03 20:56:03] [1] 1 2 3 4 5
INFO [2025-03-03 20:56:03] 
INFO [2025-03-03 20:56:03] 
INFO [2025-03-03 20:56:03] $disable.logging
INFO [2025-03-03 20:56:03] [1] TRUE
INFO [2025-03-03 20:56:03] 
INFO [2025-03-03 20:56:03] $filename
INFO [2025-03-03 20:56:03] NULL
INFO [2025-03-03 20:56:03] 
INFO [2025-03-03 20:56:04] $cat.cex
INFO [2025-03-03 20:56:04] [1] 1
INFO [2025-03-03 20:56:04] 
INFO [2025-03-03 20:56:04] $cat.col
INFO [2025-03-03 20:56:04] [1] "black"
INFO [2025-03-03 20:56:04] 
INFO [2025-03-03 20:56:04] $cat.fontface
INFO [2025-03-03 20:56:04] [1] "plain"
INFO [2025-03-03 20:56:04] 
INFO [2025-03-03 20:56:04] $cat.fontfamily
INFO [2025-03-03 20:56:04] [1] "serif"
INFO [2025-03-03 20:56:04] 
INFO [2025-03-03 20:56:04] $x
INFO [2025-03-03 20:56:04] $x$TF1
INFO [2025-03-03 20:56:04] [1] 3 4 5
INFO [2025-03-03 20:56:04] 
INFO [2025-03-03 20:56:04] $x$TF2
INFO [2025-03-03 20:56:04] [1] 1 2 4 5
INFO [2025-03-03 20:56:04] 
INFO [2025-03-03 20:56:04] $x$TF3
INFO [2025-03-03 20:56:04] [1] 3 4 5
INFO [2025-03-03 20:56:04] 
INFO [2025-03-03 20:56:04] $x$TF4
INFO [2025-03-03 20:56:04] [1] 1 2 4 5
INFO [2025-03-03 20:56:04] 
INFO [2025-03-03 20:56:04] 
INFO [2025-03-03 20:56:04] $disable.logging
INFO [2025-03-03 20:56:04] [1] TRUE
INFO [2025-03-03 20:56:04] 
INFO [2025-03-03 20:56:04] $filename
INFO [2025-03-03 20:56:04] NULL
INFO [2025-03-03 20:56:04] 
INFO [2025-03-03 20:56:04] $scaled
INFO [2025-03-03 20:56:04] [1] FALSE
INFO [2025-03-03 20:56:04] 
INFO [2025-03-03 20:56:04] $euler.d
INFO [2025-03-03 20:56:04] [1] FALSE
INFO [2025-03-03 20:56:04] 
INFO [2025-03-03 20:56:04] $cat.cex
INFO [2025-03-03 20:56:04] [1] 1
INFO [2025-03-03 20:56:04] 
INFO [2025-03-03 20:56:04] $cat.col
INFO [2025-03-03 20:56:04] [1] "black"
INFO [2025-03-03 20:56:04] 
INFO [2025-03-03 20:56:04] $cat.fontface
INFO [2025-03-03 20:56:04] [1] "plain"
INFO [2025-03-03 20:56:04] 
INFO [2025-03-03 20:56:04] $cat.fontfamily
INFO [2025-03-03 20:56:04] [1] "serif"
INFO [2025-03-03 20:56:04] 
INFO [2025-03-03 20:56:04] $x
INFO [2025-03-03 20:56:04] $x$TF1
INFO [2025-03-03 20:56:04] [1] 1 2 3
INFO [2025-03-03 20:56:04] 
INFO [2025-03-03 20:56:04] $x$TF2
INFO [2025-03-03 20:56:04] [1] 1 2 3
INFO [2025-03-03 20:56:04] 
INFO [2025-03-03 20:56:04] 
INFO [2025-03-03 20:56:04] $disable.logging
INFO [2025-03-03 20:56:04] [1] TRUE
INFO [2025-03-03 20:56:04] 
INFO [2025-03-03 20:56:04] $filename
INFO [2025-03-03 20:56:04] NULL
INFO [2025-03-03 20:56:04] 
INFO [2025-03-03 20:56:04] $scaled
INFO [2025-03-03 20:56:04] [1] FALSE
INFO [2025-03-03 20:56:04] 
INFO [2025-03-03 20:56:04] $euler.d
INFO [2025-03-03 20:56:04] [1] FALSE
INFO [2025-03-03 20:56:04] 
INFO [2025-03-03 20:56:04] $cat.cex
INFO [2025-03-03 20:56:04] [1] 1
INFO [2025-03-03 20:56:04] 
INFO [2025-03-03 20:56:04] $cat.col
INFO [2025-03-03 20:56:04] [1] "black"
INFO [2025-03-03 20:56:04] 
INFO [2025-03-03 20:56:04] $cat.fontface
INFO [2025-03-03 20:56:04] [1] "plain"
INFO [2025-03-03 20:56:04] 
INFO [2025-03-03 20:56:04] $cat.fontfamily
INFO [2025-03-03 20:56:04] [1] "serif"
INFO [2025-03-03 20:56:04] 
INFO [2025-03-03 20:56:04] $x
INFO [2025-03-03 20:56:04] $x$TF1
INFO [2025-03-03 20:56:04] [1] 4 5 6
INFO [2025-03-03 20:56:04] 
INFO [2025-03-03 20:56:04] $x$TF2
INFO [2025-03-03 20:56:04] [1] 1 2 3
INFO [2025-03-03 20:56:04] 
INFO [2025-03-03 20:56:04] 
INFO [2025-03-03 20:56:04] $disable.logging
INFO [2025-03-03 20:56:04] [1] TRUE
INFO [2025-03-03 20:56:04] 
INFO [2025-03-03 20:56:04] $filename
INFO [2025-03-03 20:56:04] NULL
INFO [2025-03-03 20:56:04] 
INFO [2025-03-03 20:56:05] $scaled
INFO [2025-03-03 20:56:05] [1] FALSE
INFO [2025-03-03 20:56:05] 
INFO [2025-03-03 20:56:05] $euler.d
INFO [2025-03-03 20:56:05] [1] FALSE
INFO [2025-03-03 20:56:05] 
INFO [2025-03-03 20:56:05] $cat.cex
INFO [2025-03-03 20:56:05] [1] 1
INFO [2025-03-03 20:56:05] 
INFO [2025-03-03 20:56:05] $cat.col
INFO [2025-03-03 20:56:05] [1] "black"
INFO [2025-03-03 20:56:05] 
INFO [2025-03-03 20:56:05] $cat.fontface
INFO [2025-03-03 20:56:05] [1] "plain"
INFO [2025-03-03 20:56:05] 
INFO [2025-03-03 20:56:05] $cat.fontfamily
INFO [2025-03-03 20:56:05] [1] "serif"
INFO [2025-03-03 20:56:05] 
INFO [2025-03-03 20:56:05] $x
INFO [2025-03-03 20:56:05] $x$TF1
INFO [2025-03-03 20:56:05] [1] 4 5 6
INFO [2025-03-03 20:56:05] 
INFO [2025-03-03 20:56:05] $x$TF2
INFO [2025-03-03 20:56:05] [1] 1 2 3
INFO [2025-03-03 20:56:05] 
INFO [2025-03-03 20:56:05] 
INFO [2025-03-03 20:56:05] $disable.logging
INFO [2025-03-03 20:56:05] [1] TRUE
INFO [2025-03-03 20:56:05] 
INFO [2025-03-03 20:56:05] $filename
INFO [2025-03-03 20:56:05] NULL
INFO [2025-03-03 20:56:05] 
INFO [2025-03-03 20:56:05] $scaled
INFO [2025-03-03 20:56:05] [1] FALSE
INFO [2025-03-03 20:56:05] 
INFO [2025-03-03 20:56:05] $euler.d
INFO [2025-03-03 20:56:05] [1] FALSE
INFO [2025-03-03 20:56:05] 
INFO [2025-03-03 20:56:05] $cat.cex
INFO [2025-03-03 20:56:05] [1] 1
INFO [2025-03-03 20:56:05] 
INFO [2025-03-03 20:56:05] $cat.col
INFO [2025-03-03 20:56:05] [1] "black"
INFO [2025-03-03 20:56:05] 
INFO [2025-03-03 20:56:05] $cat.fontface
INFO [2025-03-03 20:56:05] [1] "plain"
INFO [2025-03-03 20:56:05] 
INFO [2025-03-03 20:56:05] $cat.fontfamily
INFO [2025-03-03 20:56:05] [1] "serif"
INFO [2025-03-03 20:56:05] 
INFO [2025-03-03 20:56:05] $x
INFO [2025-03-03 20:56:05] $x$TF1
INFO [2025-03-03 20:56:05] [1] 4 5 6
INFO [2025-03-03 20:56:05] 
INFO [2025-03-03 20:56:05] $x$TF2
INFO [2025-03-03 20:56:05] [1] 1 2 3
INFO [2025-03-03 20:56:05] 
INFO [2025-03-03 20:56:05] $x$TF3
INFO [2025-03-03 20:56:05] [1] 2 3 6
INFO [2025-03-03 20:56:05] 
INFO [2025-03-03 20:56:05] 
INFO [2025-03-03 20:56:05] $disable.logging
INFO [2025-03-03 20:56:05] [1] TRUE
INFO [2025-03-03 20:56:05] 
INFO [2025-03-03 20:56:05] $filename
INFO [2025-03-03 20:56:05] NULL
INFO [2025-03-03 20:56:05] 
INFO [2025-03-03 20:56:05] $scaled
INFO [2025-03-03 20:56:05] [1] FALSE
INFO [2025-03-03 20:56:05] 
INFO [2025-03-03 20:56:05] $euler.d
INFO [2025-03-03 20:56:05] [1] FALSE
INFO [2025-03-03 20:56:05] 
INFO [2025-03-03 20:56:05] $cat.cex
INFO [2025-03-03 20:56:05] [1] 1
INFO [2025-03-03 20:56:05] 
INFO [2025-03-03 20:56:05] $cat.col
INFO [2025-03-03 20:56:05] [1] "black"
INFO [2025-03-03 20:56:05] 
INFO [2025-03-03 20:56:05] $cat.fontface
INFO [2025-03-03 20:56:05] [1] "plain"
INFO [2025-03-03 20:56:05] 
INFO [2025-03-03 20:56:05] $cat.fontfamily
INFO [2025-03-03 20:56:05] [1] "serif"
INFO [2025-03-03 20:56:05] 
INFO [2025-03-03 20:56:05] $x
INFO [2025-03-03 20:56:05] $x$TF1
INFO [2025-03-03 20:56:05] [1] 3 4 5
INFO [2025-03-03 20:56:05] 
INFO [2025-03-03 20:56:05] $x$TF2
INFO [2025-03-03 20:56:05] [1] 1 2 5
INFO [2025-03-03 20:56:05] 
INFO [2025-03-03 20:56:05] $x$TF3
INFO [2025-03-03 20:56:05] [1] 1 2 5
INFO [2025-03-03 20:56:05] 
INFO [2025-03-03 20:56:05] 
INFO [2025-03-03 20:56:05] $disable.logging
INFO [2025-03-03 20:56:05] [1] TRUE
INFO [2025-03-03 20:56:05] 
INFO [2025-03-03 20:56:05] $filename
INFO [2025-03-03 20:56:05] NULL
INFO [2025-03-03 20:56:05] 
INFO [2025-03-03 20:56:06] $scaled
INFO [2025-03-03 20:56:06] [1] FALSE
INFO [2025-03-03 20:56:06] 
INFO [2025-03-03 20:56:06] $euler.d
INFO [2025-03-03 20:56:06] [1] FALSE
INFO [2025-03-03 20:56:06] 
INFO [2025-03-03 20:56:06] $cat.cex
INFO [2025-03-03 20:56:06] [1] 1
INFO [2025-03-03 20:56:06] 
INFO [2025-03-03 20:56:06] $cat.col
INFO [2025-03-03 20:56:06] [1] "black"
INFO [2025-03-03 20:56:06] 
INFO [2025-03-03 20:56:06] $cat.fontface
INFO [2025-03-03 20:56:06] [1] "plain"
INFO [2025-03-03 20:56:06] 
INFO [2025-03-03 20:56:06] $cat.fontfamily
INFO [2025-03-03 20:56:06] [1] "serif"
INFO [2025-03-03 20:56:06] 
INFO [2025-03-03 20:56:06] $x
INFO [2025-03-03 20:56:06] $x$TF1
INFO [2025-03-03 20:56:06] [1] 3 4 5
INFO [2025-03-03 20:56:06] 
INFO [2025-03-03 20:56:06] $x$TF2
INFO [2025-03-03 20:56:06] [1] 1 2 5
INFO [2025-03-03 20:56:06] 
INFO [2025-03-03 20:56:06] $x$TF3
INFO [2025-03-03 20:56:06] [1] 1 2 5
INFO [2025-03-03 20:56:06] 
INFO [2025-03-03 20:56:06] $x$TF4
INFO [2025-03-03 20:56:06] [1] 1 2 5
INFO [2025-03-03 20:56:06] 
INFO [2025-03-03 20:56:06] 
INFO [2025-03-03 20:56:06] $disable.logging
INFO [2025-03-03 20:56:06] [1] TRUE
INFO [2025-03-03 20:56:06] 
INFO [2025-03-03 20:56:06] $filename
INFO [2025-03-03 20:56:06] NULL
INFO [2025-03-03 20:56:06] 
[ 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 
153.309   6.659 162.980

Example timings

ChIPpeakAnno.Rcheck/ChIPpeakAnno-Ex.timings

name	user	system	elapsed
ChIPpeakAnno-package	0.001	0.001	0.000
ExonPlusUtr.human.GRCh37	3.995	0.243	4.240
HOT.spots	0.131	0.012	0.142
IDRfilter	0.001	0.000	0.000
Peaks.Ste12.Replicate1	0.047	0.000	0.048
Peaks.Ste12.Replicate2	0.012	0.000	0.012
Peaks.Ste12.Replicate3	0.011	0.000	0.011
TSS.human.GRCh37	0.164	0.013	0.179
TSS.human.GRCh38	0.143	0.000	0.143
TSS.human.NCBI36	0.105	0.007	0.110
TSS.mouse.GRCm38	0.095	0.010	0.104
TSS.mouse.NCBIM37	0.086	0.008	0.095
TSS.rat.RGSC3.4	0.077	0.003	0.080
TSS.rat.Rnor_5.0	0.063	0.005	0.068
TSS.zebrafish.Zv8	0.065	0.006	0.072
TSS.zebrafish.Zv9	0.079	0.008	0.089
addAncestors	0.952	0.043	0.997
addGeneIDs	0.863	0.032	0.896
addMetadata	1.002	0.092	1.095
annoGR	0.001	0.001	0.000
annoPeaks	3.233	0.252	4.790
annotatePeakInBatch	12.050	1.144	13.195
annotatedPeak	0.059	0.009	0.068
assignChromosomeRegion	0.001	0.000	0.000
bdp	0	0	0
binOverFeature	0.692	0.063	0.755
binOverGene	0	0	0
binOverRegions	0	0	0
condenseMatrixByColnames	0.009	0.002	0.010
convert2EntrezID	0.417	0.004	0.421
countPatternInSeqs	0.141	0.003	0.144
cumulativePercentage	0	0	0
downstreams	0.021	0.000	0.020
egOrgMap	0	0	0
enrichedGO	0.002	0.000	0.002
enrichmentPlot	0.427	0.009	0.436
estFragmentLength	0.001	0.000	0.000
estLibSize	0.000	0.000	0.001
featureAlignedDistribution	0.206	0.004	0.210
featureAlignedExtendSignal	0.001	0.000	0.001
featureAlignedHeatmap	0.285	0.005	0.291
featureAlignedSignal	0.161	0.009	0.170
findEnhancers	22.002	0.696	22.698
findMotifsInPromoterSeqs	12.855	0.322	13.197
findOverlappingPeaks	0.001	0.000	0.000
findOverlapsOfPeaks	1.589	0.008	1.598
genomicElementDistribution	0.001	0.000	0.001
genomicElementUpSetR	0.001	0.000	0.000
getAllPeakSequence	0.520	0.008	0.529
getAnnotation	0.001	0.000	0.001
getEnrichedGO	0.007	0.001	0.008
getEnrichedPATH	0	0	0
getGO	0	0	0
getGeneSeq	0.001	0.000	0.001
getUniqueGOidCount	0.001	0.001	0.001
getVennCounts	0	0	0
hyperGtest	0	0	0
makeVennDiagram	0.002	0.000	0.002
mergePlusMinusPeaks	0.001	0.000	0.001
metagenePlot	1.861	0.048	1.909
myPeakList	0.016	0.000	0.016
oligoFrequency	0.103	0.001	0.104
oligoSummary	0.001	0.000	0.000
peakPermTest	0.001	0.000	0.001
peaks1	0.006	0.001	0.007
peaks2	0.007	0.000	0.007
peaks3	0.007	0.000	0.007
peaksNearBDP	0.001	0.000	0.000
pie1	0.004	0.001	0.004
plotBinOverRegions	0	0	0
preparePool	0.000	0.000	0.001
reCenterPeaks	0.022	0.000	0.022
summarizeOverlapsByBins	5.647	0.603	5.954
summarizePatternInPeaks	1.414	0.226	1.641
tileCount	0.188	0.187	0.349
tileGRanges	0.138	0.122	0.035
toGRanges	0.068	0.018	0.086
translatePattern	0.001	0.000	0.001
wgEncodeTfbsV3	0.220	0.006	0.227
write2FASTA	0.012	0.002	0.014
xget	0.091	0.010	0.101