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This page was generated on 2024-11-20 12:02 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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 337/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPpeakAnno 3.40.0  (landing page)
Jianhong Ou
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/ChIPpeakAnno
git_branch: RELEASE_3_20
git_last_commit: faf2e4f
git_last_commit_date: 2024-10-29 09:32:01 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
palomino8Windows 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
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for ChIPpeakAnno on teran2

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: 2024-11-20 00:13:45 -0500 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 00:36:24 -0500 (Wed, 20 Nov 2024)
EllapsedTime: 1359.4 seconds
RetCode: 0
Status:   OK  
CheckDir: ChIPpeakAnno.Rcheck
Warnings: 0

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 ‘/media/volume/teran2_disk/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 24.04.1 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            17.564  0.252  18.547
annotatePeakInBatch      10.624  0.323  11.470
findMotifsInPromoterSeqs 10.759  0.073  11.578
summarizeOverlapsByBins   6.188  0.384   6.617
annoPeaks                 2.159  0.164   5.158
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/media/volume/teran2_disk/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 ‘/media/volume/teran2_disk/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 [2024-11-20 00:23:07] $cat.cex
INFO [2024-11-20 00:23:07] [1] 1
INFO [2024-11-20 00:23:07] 
INFO [2024-11-20 00:23:07] $cat.col
INFO [2024-11-20 00:23:07] [1] "black"
INFO [2024-11-20 00:23:07] 
INFO [2024-11-20 00:23:07] $cat.fontface
INFO [2024-11-20 00:23:07] [1] "plain"
INFO [2024-11-20 00:23:07] 
INFO [2024-11-20 00:23:07] $cat.fontfamily
INFO [2024-11-20 00:23:07] [1] "serif"
INFO [2024-11-20 00:23:07] 
INFO [2024-11-20 00:23:07] $x
INFO [2024-11-20 00:23:07] $x$TF1
INFO [2024-11-20 00:23:07] [1] 3 4 5
INFO [2024-11-20 00:23:07] 
INFO [2024-11-20 00:23:07] $x$TF2
INFO [2024-11-20 00:23:07] [1] 1 2 3 4 5
INFO [2024-11-20 00:23:07] 
INFO [2024-11-20 00:23:07] 
INFO [2024-11-20 00:23:07] $disable.logging
INFO [2024-11-20 00:23:07] [1] TRUE
INFO [2024-11-20 00:23:07] 
INFO [2024-11-20 00:23:07] $filename
INFO [2024-11-20 00:23:07] NULL
INFO [2024-11-20 00:23:07] 
INFO [2024-11-20 00:23:07] $cat.cex
INFO [2024-11-20 00:23:07] [1] 1
INFO [2024-11-20 00:23:07] 
INFO [2024-11-20 00:23:07] $cat.col
INFO [2024-11-20 00:23:07] [1] "black"
INFO [2024-11-20 00:23:07] 
INFO [2024-11-20 00:23:07] $cat.fontface
INFO [2024-11-20 00:23:07] [1] "plain"
INFO [2024-11-20 00:23:07] 
INFO [2024-11-20 00:23:07] $cat.fontfamily
INFO [2024-11-20 00:23:07] [1] "serif"
INFO [2024-11-20 00:23:07] 
INFO [2024-11-20 00:23:07] $x
INFO [2024-11-20 00:23:07] $x$TF1
INFO [2024-11-20 00:23:07] [1] 3 4 5
INFO [2024-11-20 00:23:07] 
INFO [2024-11-20 00:23:07] $x$TF2
INFO [2024-11-20 00:23:07] [1] 1 2 4 5
INFO [2024-11-20 00:23:07] 
INFO [2024-11-20 00:23:07] $x$TF3
INFO [2024-11-20 00:23:07] [1] 3 4 5
INFO [2024-11-20 00:23:07] 
INFO [2024-11-20 00:23:07] $x$TF4
INFO [2024-11-20 00:23:07] [1] 1 2 4 5
INFO [2024-11-20 00:23:07] 
INFO [2024-11-20 00:23:07] 
INFO [2024-11-20 00:23:07] $disable.logging
INFO [2024-11-20 00:23:07] [1] TRUE
INFO [2024-11-20 00:23:07] 
INFO [2024-11-20 00:23:07] $filename
INFO [2024-11-20 00:23:07] NULL
INFO [2024-11-20 00:23:07] 
INFO [2024-11-20 00:23:07] $scaled
INFO [2024-11-20 00:23:07] [1] FALSE
INFO [2024-11-20 00:23:07] 
INFO [2024-11-20 00:23:07] $euler.d
INFO [2024-11-20 00:23:07] [1] FALSE
INFO [2024-11-20 00:23:07] 
INFO [2024-11-20 00:23:07] $cat.cex
INFO [2024-11-20 00:23:07] [1] 1
INFO [2024-11-20 00:23:07] 
INFO [2024-11-20 00:23:07] $cat.col
INFO [2024-11-20 00:23:07] [1] "black"
INFO [2024-11-20 00:23:07] 
INFO [2024-11-20 00:23:07] $cat.fontface
INFO [2024-11-20 00:23:07] [1] "plain"
INFO [2024-11-20 00:23:07] 
INFO [2024-11-20 00:23:07] $cat.fontfamily
INFO [2024-11-20 00:23:07] [1] "serif"
INFO [2024-11-20 00:23:07] 
INFO [2024-11-20 00:23:07] $x
INFO [2024-11-20 00:23:07] $x$TF1
INFO [2024-11-20 00:23:07] [1] 1 2 3
INFO [2024-11-20 00:23:07] 
INFO [2024-11-20 00:23:07] $x$TF2
INFO [2024-11-20 00:23:07] [1] 1 2 3
INFO [2024-11-20 00:23:07] 
INFO [2024-11-20 00:23:07] 
INFO [2024-11-20 00:23:07] $disable.logging
INFO [2024-11-20 00:23:07] [1] TRUE
INFO [2024-11-20 00:23:07] 
INFO [2024-11-20 00:23:07] $filename
INFO [2024-11-20 00:23:07] NULL
INFO [2024-11-20 00:23:07] 
INFO [2024-11-20 00:23:07] $scaled
INFO [2024-11-20 00:23:07] [1] FALSE
INFO [2024-11-20 00:23:07] 
INFO [2024-11-20 00:23:07] $euler.d
INFO [2024-11-20 00:23:07] [1] FALSE
INFO [2024-11-20 00:23:07] 
INFO [2024-11-20 00:23:07] $cat.cex
INFO [2024-11-20 00:23:07] [1] 1
INFO [2024-11-20 00:23:07] 
INFO [2024-11-20 00:23:07] $cat.col
INFO [2024-11-20 00:23:07] [1] "black"
INFO [2024-11-20 00:23:07] 
INFO [2024-11-20 00:23:07] $cat.fontface
INFO [2024-11-20 00:23:07] [1] "plain"
INFO [2024-11-20 00:23:07] 
INFO [2024-11-20 00:23:07] $cat.fontfamily
INFO [2024-11-20 00:23:07] [1] "serif"
INFO [2024-11-20 00:23:07] 
INFO [2024-11-20 00:23:07] $x
INFO [2024-11-20 00:23:07] $x$TF1
INFO [2024-11-20 00:23:07] [1] 4 5 6
INFO [2024-11-20 00:23:07] 
INFO [2024-11-20 00:23:07] $x$TF2
INFO [2024-11-20 00:23:07] [1] 1 2 3
INFO [2024-11-20 00:23:07] 
INFO [2024-11-20 00:23:07] 
INFO [2024-11-20 00:23:07] $disable.logging
INFO [2024-11-20 00:23:07] [1] TRUE
INFO [2024-11-20 00:23:07] 
INFO [2024-11-20 00:23:07] $filename
INFO [2024-11-20 00:23:07] NULL
INFO [2024-11-20 00:23:07] 
INFO [2024-11-20 00:23:08] $scaled
INFO [2024-11-20 00:23:08] [1] FALSE
INFO [2024-11-20 00:23:08] 
INFO [2024-11-20 00:23:08] $euler.d
INFO [2024-11-20 00:23:08] [1] FALSE
INFO [2024-11-20 00:23:08] 
INFO [2024-11-20 00:23:08] $cat.cex
INFO [2024-11-20 00:23:08] [1] 1
INFO [2024-11-20 00:23:08] 
INFO [2024-11-20 00:23:08] $cat.col
INFO [2024-11-20 00:23:08] [1] "black"
INFO [2024-11-20 00:23:08] 
INFO [2024-11-20 00:23:08] $cat.fontface
INFO [2024-11-20 00:23:08] [1] "plain"
INFO [2024-11-20 00:23:08] 
INFO [2024-11-20 00:23:08] $cat.fontfamily
INFO [2024-11-20 00:23:08] [1] "serif"
INFO [2024-11-20 00:23:08] 
INFO [2024-11-20 00:23:08] $x
INFO [2024-11-20 00:23:08] $x$TF1
INFO [2024-11-20 00:23:08] [1] 4 5 6
INFO [2024-11-20 00:23:08] 
INFO [2024-11-20 00:23:08] $x$TF2
INFO [2024-11-20 00:23:08] [1] 1 2 3
INFO [2024-11-20 00:23:08] 
INFO [2024-11-20 00:23:08] 
INFO [2024-11-20 00:23:08] $disable.logging
INFO [2024-11-20 00:23:08] [1] TRUE
INFO [2024-11-20 00:23:08] 
INFO [2024-11-20 00:23:08] $filename
INFO [2024-11-20 00:23:08] NULL
INFO [2024-11-20 00:23:08] 
INFO [2024-11-20 00:23:08] $scaled
INFO [2024-11-20 00:23:08] [1] FALSE
INFO [2024-11-20 00:23:08] 
INFO [2024-11-20 00:23:08] $euler.d
INFO [2024-11-20 00:23:08] [1] FALSE
INFO [2024-11-20 00:23:08] 
INFO [2024-11-20 00:23:08] $cat.cex
INFO [2024-11-20 00:23:08] [1] 1
INFO [2024-11-20 00:23:08] 
INFO [2024-11-20 00:23:08] $cat.col
INFO [2024-11-20 00:23:08] [1] "black"
INFO [2024-11-20 00:23:08] 
INFO [2024-11-20 00:23:08] $cat.fontface
INFO [2024-11-20 00:23:08] [1] "plain"
INFO [2024-11-20 00:23:08] 
INFO [2024-11-20 00:23:08] $cat.fontfamily
INFO [2024-11-20 00:23:08] [1] "serif"
INFO [2024-11-20 00:23:08] 
INFO [2024-11-20 00:23:08] $x
INFO [2024-11-20 00:23:08] $x$TF1
INFO [2024-11-20 00:23:08] [1] 4 5 6
INFO [2024-11-20 00:23:08] 
INFO [2024-11-20 00:23:08] $x$TF2
INFO [2024-11-20 00:23:08] [1] 1 2 3
INFO [2024-11-20 00:23:08] 
INFO [2024-11-20 00:23:08] $x$TF3
INFO [2024-11-20 00:23:08] [1] 2 3 6
INFO [2024-11-20 00:23:08] 
INFO [2024-11-20 00:23:08] 
INFO [2024-11-20 00:23:08] $disable.logging
INFO [2024-11-20 00:23:08] [1] TRUE
INFO [2024-11-20 00:23:08] 
INFO [2024-11-20 00:23:08] $filename
INFO [2024-11-20 00:23:08] NULL
INFO [2024-11-20 00:23:08] 
INFO [2024-11-20 00:23:08] $scaled
INFO [2024-11-20 00:23:08] [1] FALSE
INFO [2024-11-20 00:23:08] 
INFO [2024-11-20 00:23:08] $euler.d
INFO [2024-11-20 00:23:08] [1] FALSE
INFO [2024-11-20 00:23:08] 
INFO [2024-11-20 00:23:08] $cat.cex
INFO [2024-11-20 00:23:08] [1] 1
INFO [2024-11-20 00:23:08] 
INFO [2024-11-20 00:23:08] $cat.col
INFO [2024-11-20 00:23:08] [1] "black"
INFO [2024-11-20 00:23:08] 
INFO [2024-11-20 00:23:08] $cat.fontface
INFO [2024-11-20 00:23:08] [1] "plain"
INFO [2024-11-20 00:23:08] 
INFO [2024-11-20 00:23:08] $cat.fontfamily
INFO [2024-11-20 00:23:08] [1] "serif"
INFO [2024-11-20 00:23:08] 
INFO [2024-11-20 00:23:08] $x
INFO [2024-11-20 00:23:08] $x$TF1
INFO [2024-11-20 00:23:08] [1] 3 4 5
INFO [2024-11-20 00:23:08] 
INFO [2024-11-20 00:23:08] $x$TF2
INFO [2024-11-20 00:23:08] [1] 1 2 5
INFO [2024-11-20 00:23:08] 
INFO [2024-11-20 00:23:08] $x$TF3
INFO [2024-11-20 00:23:08] [1] 1 2 5
INFO [2024-11-20 00:23:08] 
INFO [2024-11-20 00:23:08] 
INFO [2024-11-20 00:23:08] $disable.logging
INFO [2024-11-20 00:23:08] [1] TRUE
INFO [2024-11-20 00:23:08] 
INFO [2024-11-20 00:23:08] $filename
INFO [2024-11-20 00:23:08] NULL
INFO [2024-11-20 00:23:08] 
INFO [2024-11-20 00:23:08] $scaled
INFO [2024-11-20 00:23:08] [1] FALSE
INFO [2024-11-20 00:23:08] 
INFO [2024-11-20 00:23:08] $euler.d
INFO [2024-11-20 00:23:08] [1] FALSE
INFO [2024-11-20 00:23:08] 
INFO [2024-11-20 00:23:08] $cat.cex
INFO [2024-11-20 00:23:08] [1] 1
INFO [2024-11-20 00:23:08] 
INFO [2024-11-20 00:23:08] $cat.col
INFO [2024-11-20 00:23:08] [1] "black"
INFO [2024-11-20 00:23:08] 
INFO [2024-11-20 00:23:08] $cat.fontface
INFO [2024-11-20 00:23:08] [1] "plain"
INFO [2024-11-20 00:23:08] 
INFO [2024-11-20 00:23:08] $cat.fontfamily
INFO [2024-11-20 00:23:08] [1] "serif"
INFO [2024-11-20 00:23:08] 
INFO [2024-11-20 00:23:08] $x
INFO [2024-11-20 00:23:08] $x$TF1
INFO [2024-11-20 00:23:08] [1] 3 4 5
INFO [2024-11-20 00:23:08] 
INFO [2024-11-20 00:23:08] $x$TF2
INFO [2024-11-20 00:23:08] [1] 1 2 5
INFO [2024-11-20 00:23:08] 
INFO [2024-11-20 00:23:08] $x$TF3
INFO [2024-11-20 00:23:08] [1] 1 2 5
INFO [2024-11-20 00:23:08] 
INFO [2024-11-20 00:23:08] $x$TF4
INFO [2024-11-20 00:23:08] [1] 1 2 5
INFO [2024-11-20 00:23:08] 
INFO [2024-11-20 00:23:08] 
INFO [2024-11-20 00:23:08] $disable.logging
INFO [2024-11-20 00:23:08] [1] TRUE
INFO [2024-11-20 00:23:08] 
INFO [2024-11-20 00:23:08] $filename
INFO [2024-11-20 00:23:08] NULL
INFO [2024-11-20 00:23:08] 
[ 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 
129.946   2.178 174.305 

Example timings

ChIPpeakAnno.Rcheck/ChIPpeakAnno-Ex.timings

nameusersystemelapsed
ChIPpeakAnno-package0.0000.0000.001
ExonPlusUtr.human.GRCh373.4280.1713.634
HOT.spots0.1040.0090.115
IDRfilter0.0000.0000.001
Peaks.Ste12.Replicate10.0360.0010.036
Peaks.Ste12.Replicate20.0060.0020.008
Peaks.Ste12.Replicate30.0060.0020.010
TSS.human.GRCh370.1310.0130.145
TSS.human.GRCh380.1050.0020.107
TSS.human.NCBI360.0810.0050.085
TSS.mouse.GRCm380.0780.0080.088
TSS.mouse.NCBIM370.0660.0080.075
TSS.rat.RGSC3.40.0590.0060.069
TSS.rat.Rnor_5.00.0430.0130.061
TSS.zebrafish.Zv80.0560.0050.064
TSS.zebrafish.Zv90.0610.0120.075
addAncestors0.6300.0280.662
addGeneIDs0.6640.0340.743
addMetadata0.7220.0930.818
annoGR000
annoPeaks2.1590.1645.158
annotatePeakInBatch10.624 0.32311.470
annotatedPeak0.0470.0010.095
assignChromosomeRegion0.0010.0000.001
bdp000
binOverFeature1.1570.0021.227
binOverGene000
binOverRegions0.0010.0000.001
condenseMatrixByColnames0.0070.0000.007
convert2EntrezID0.2990.0000.418
countPatternInSeqs0.0980.0020.101
cumulativePercentage000
downstreams0.0160.0000.017
egOrgMap0.0010.0000.000
enrichedGO0.0020.0000.002
enrichmentPlot0.3290.0010.334
estFragmentLength000
estLibSize0.0000.0010.000
featureAlignedDistribution0.1460.0010.148
featureAlignedExtendSignal000
featureAlignedHeatmap0.2070.0000.207
featureAlignedSignal0.1150.0150.130
findEnhancers17.564 0.25218.547
findMotifsInPromoterSeqs10.759 0.07311.578
findOverlappingPeaks0.0010.0000.001
findOverlapsOfPeaks1.6590.0051.743
genomicElementDistribution0.0010.0000.001
genomicElementUpSetR0.0010.0000.001
getAllPeakSequence0.3330.0040.422
getAnnotation000
getEnrichedGO0.0070.0000.007
getEnrichedPATH000
getGO000
getGeneSeq0.0010.0000.001
getUniqueGOidCount0.0000.0000.001
getVennCounts0.0010.0000.000
hyperGtest000
makeVennDiagram0.0010.0000.001
mergePlusMinusPeaks0.0000.0000.001
metagenePlot1.3290.0441.412
myPeakList0.0140.0010.021
oligoFrequency0.0530.0020.055
oligoSummary0.0000.0000.001
peakPermTest0.0010.0000.001
peaks10.0060.0010.007
peaks20.0040.0020.006
peaks30.0040.0020.006
peaksNearBDP000
pie10.0020.0010.003
plotBinOverRegions0.0000.0010.000
preparePool0.0000.0000.001
reCenterPeaks0.0160.0000.017
summarizeOverlapsByBins6.1880.3846.617
summarizePatternInPeaks0.9680.1971.173
tileCount0.1560.2210.557
tileGRanges0.1140.1340.058
toGRanges0.0560.0110.095
translatePattern0.0000.0000.001
wgEncodeTfbsV30.1670.0070.174
write2FASTA0.0110.0020.013
xget0.0600.0040.064