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This page was generated on 2024-11-20 12:07 -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 kunpeng2

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: ChIPpeakAnno
Version: 3.40.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ChIPpeakAnno_3.40.0.tar.gz
StartedAt: 2024-11-20 06:10:55 -0000 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 06:24:59 -0000 (Wed, 20 Nov 2024)
EllapsedTime: 843.5 seconds
RetCode: 0
Status:   OK  
CheckDir: ChIPpeakAnno.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ChIPpeakAnno_3.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/ChIPpeakAnno.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChIPpeakAnno/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChIPpeakAnno’ version ‘3.40.0’
* 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            32.871  0.658  33.598
findMotifsInPromoterSeqs 19.407  0.188  19.699
annotatePeakInBatch      17.274  1.078  18.389
summarizeOverlapsByBins   6.688  0.477   6.841
annoPeaks                 3.872  0.311  20.137
* 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
  ‘/home/biocbuild/bbs-3.20-bioc/meat/ChIPpeakAnno.Rcheck/00check.log’
for details.


Installation output

ChIPpeakAnno.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL ChIPpeakAnno
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4.1/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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 06:24:37] $cat.cex
INFO [2024-11-20 06:24:37] [1] 1
INFO [2024-11-20 06:24:37] 
INFO [2024-11-20 06:24:37] $cat.col
INFO [2024-11-20 06:24:37] [1] "black"
INFO [2024-11-20 06:24:37] 
INFO [2024-11-20 06:24:37] $cat.fontface
INFO [2024-11-20 06:24:37] [1] "plain"
INFO [2024-11-20 06:24:37] 
INFO [2024-11-20 06:24:37] $cat.fontfamily
INFO [2024-11-20 06:24:37] [1] "serif"
INFO [2024-11-20 06:24:37] 
INFO [2024-11-20 06:24:37] $x
INFO [2024-11-20 06:24:37] $x$TF1
INFO [2024-11-20 06:24:37] [1] 3 4 5
INFO [2024-11-20 06:24:37] 
INFO [2024-11-20 06:24:37] $x$TF2
INFO [2024-11-20 06:24:37] [1] 1 2 3 4 5
INFO [2024-11-20 06:24:37] 
INFO [2024-11-20 06:24:37] 
INFO [2024-11-20 06:24:37] $disable.logging
INFO [2024-11-20 06:24:37] [1] TRUE
INFO [2024-11-20 06:24:37] 
INFO [2024-11-20 06:24:37] $filename
INFO [2024-11-20 06:24:37] NULL
INFO [2024-11-20 06:24:37] 
INFO [2024-11-20 06:24:37] $cat.cex
INFO [2024-11-20 06:24:37] [1] 1
INFO [2024-11-20 06:24:37] 
INFO [2024-11-20 06:24:37] $cat.col
INFO [2024-11-20 06:24:37] [1] "black"
INFO [2024-11-20 06:24:37] 
INFO [2024-11-20 06:24:37] $cat.fontface
INFO [2024-11-20 06:24:37] [1] "plain"
INFO [2024-11-20 06:24:37] 
INFO [2024-11-20 06:24:37] $cat.fontfamily
INFO [2024-11-20 06:24:37] [1] "serif"
INFO [2024-11-20 06:24:37] 
INFO [2024-11-20 06:24:37] $x
INFO [2024-11-20 06:24:37] $x$TF1
INFO [2024-11-20 06:24:37] [1] 3 4 5
INFO [2024-11-20 06:24:37] 
INFO [2024-11-20 06:24:37] $x$TF2
INFO [2024-11-20 06:24:37] [1] 1 2 4 5
INFO [2024-11-20 06:24:37] 
INFO [2024-11-20 06:24:37] $x$TF3
INFO [2024-11-20 06:24:37] [1] 3 4 5
INFO [2024-11-20 06:24:37] 
INFO [2024-11-20 06:24:37] $x$TF4
INFO [2024-11-20 06:24:37] [1] 1 2 4 5
INFO [2024-11-20 06:24:37] 
INFO [2024-11-20 06:24:37] 
INFO [2024-11-20 06:24:37] $disable.logging
INFO [2024-11-20 06:24:37] [1] TRUE
INFO [2024-11-20 06:24:37] 
INFO [2024-11-20 06:24:37] $filename
INFO [2024-11-20 06:24:37] NULL
INFO [2024-11-20 06:24:37] 
INFO [2024-11-20 06:24:38] $scaled
INFO [2024-11-20 06:24:38] [1] FALSE
INFO [2024-11-20 06:24:38] 
INFO [2024-11-20 06:24:38] $euler.d
INFO [2024-11-20 06:24:38] [1] FALSE
INFO [2024-11-20 06:24:38] 
INFO [2024-11-20 06:24:38] $cat.cex
INFO [2024-11-20 06:24:38] [1] 1
INFO [2024-11-20 06:24:38] 
INFO [2024-11-20 06:24:38] $cat.col
INFO [2024-11-20 06:24:38] [1] "black"
INFO [2024-11-20 06:24:38] 
INFO [2024-11-20 06:24:38] $cat.fontface
INFO [2024-11-20 06:24:38] [1] "plain"
INFO [2024-11-20 06:24:38] 
INFO [2024-11-20 06:24:38] $cat.fontfamily
INFO [2024-11-20 06:24:38] [1] "serif"
INFO [2024-11-20 06:24:38] 
INFO [2024-11-20 06:24:38] $x
INFO [2024-11-20 06:24:38] $x$TF1
INFO [2024-11-20 06:24:38] [1] 1 2 3
INFO [2024-11-20 06:24:38] 
INFO [2024-11-20 06:24:38] $x$TF2
INFO [2024-11-20 06:24:38] [1] 1 2 3
INFO [2024-11-20 06:24:38] 
INFO [2024-11-20 06:24:38] 
INFO [2024-11-20 06:24:38] $disable.logging
INFO [2024-11-20 06:24:38] [1] TRUE
INFO [2024-11-20 06:24:38] 
INFO [2024-11-20 06:24:38] $filename
INFO [2024-11-20 06:24:38] NULL
INFO [2024-11-20 06:24:38] 
INFO [2024-11-20 06:24:38] $scaled
INFO [2024-11-20 06:24:38] [1] FALSE
INFO [2024-11-20 06:24:38] 
INFO [2024-11-20 06:24:38] $euler.d
INFO [2024-11-20 06:24:38] [1] FALSE
INFO [2024-11-20 06:24:38] 
INFO [2024-11-20 06:24:38] $cat.cex
INFO [2024-11-20 06:24:38] [1] 1
INFO [2024-11-20 06:24:38] 
INFO [2024-11-20 06:24:38] $cat.col
INFO [2024-11-20 06:24:38] [1] "black"
INFO [2024-11-20 06:24:38] 
INFO [2024-11-20 06:24:38] $cat.fontface
INFO [2024-11-20 06:24:38] [1] "plain"
INFO [2024-11-20 06:24:38] 
INFO [2024-11-20 06:24:38] $cat.fontfamily
INFO [2024-11-20 06:24:38] [1] "serif"
INFO [2024-11-20 06:24:38] 
INFO [2024-11-20 06:24:38] $x
INFO [2024-11-20 06:24:38] $x$TF1
INFO [2024-11-20 06:24:38] [1] 4 5 6
INFO [2024-11-20 06:24:38] 
INFO [2024-11-20 06:24:38] $x$TF2
INFO [2024-11-20 06:24:38] [1] 1 2 3
INFO [2024-11-20 06:24:38] 
INFO [2024-11-20 06:24:38] 
INFO [2024-11-20 06:24:38] $disable.logging
INFO [2024-11-20 06:24:38] [1] TRUE
INFO [2024-11-20 06:24:38] 
INFO [2024-11-20 06:24:38] $filename
INFO [2024-11-20 06:24:38] NULL
INFO [2024-11-20 06:24:38] 
INFO [2024-11-20 06:24:38] $scaled
INFO [2024-11-20 06:24:38] [1] FALSE
INFO [2024-11-20 06:24:38] 
INFO [2024-11-20 06:24:38] $euler.d
INFO [2024-11-20 06:24:38] [1] FALSE
INFO [2024-11-20 06:24:38] 
INFO [2024-11-20 06:24:38] $cat.cex
INFO [2024-11-20 06:24:38] [1] 1
INFO [2024-11-20 06:24:38] 
INFO [2024-11-20 06:24:38] $cat.col
INFO [2024-11-20 06:24:38] [1] "black"
INFO [2024-11-20 06:24:38] 
INFO [2024-11-20 06:24:38] $cat.fontface
INFO [2024-11-20 06:24:38] [1] "plain"
INFO [2024-11-20 06:24:38] 
INFO [2024-11-20 06:24:38] $cat.fontfamily
INFO [2024-11-20 06:24:38] [1] "serif"
INFO [2024-11-20 06:24:38] 
INFO [2024-11-20 06:24:38] $x
INFO [2024-11-20 06:24:38] $x$TF1
INFO [2024-11-20 06:24:38] [1] 4 5 6
INFO [2024-11-20 06:24:38] 
INFO [2024-11-20 06:24:38] $x$TF2
INFO [2024-11-20 06:24:38] [1] 1 2 3
INFO [2024-11-20 06:24:38] 
INFO [2024-11-20 06:24:38] 
INFO [2024-11-20 06:24:38] $disable.logging
INFO [2024-11-20 06:24:38] [1] TRUE
INFO [2024-11-20 06:24:38] 
INFO [2024-11-20 06:24:38] $filename
INFO [2024-11-20 06:24:38] NULL
INFO [2024-11-20 06:24:38] 
INFO [2024-11-20 06:24:39] $scaled
INFO [2024-11-20 06:24:39] [1] FALSE
INFO [2024-11-20 06:24:39] 
INFO [2024-11-20 06:24:39] $euler.d
INFO [2024-11-20 06:24:39] [1] FALSE
INFO [2024-11-20 06:24:39] 
INFO [2024-11-20 06:24:39] $cat.cex
INFO [2024-11-20 06:24:39] [1] 1
INFO [2024-11-20 06:24:39] 
INFO [2024-11-20 06:24:39] $cat.col
INFO [2024-11-20 06:24:39] [1] "black"
INFO [2024-11-20 06:24:39] 
INFO [2024-11-20 06:24:39] $cat.fontface
INFO [2024-11-20 06:24:39] [1] "plain"
INFO [2024-11-20 06:24:39] 
INFO [2024-11-20 06:24:39] $cat.fontfamily
INFO [2024-11-20 06:24:39] [1] "serif"
INFO [2024-11-20 06:24:39] 
INFO [2024-11-20 06:24:39] $x
INFO [2024-11-20 06:24:39] $x$TF1
INFO [2024-11-20 06:24:39] [1] 4 5 6
INFO [2024-11-20 06:24:39] 
INFO [2024-11-20 06:24:39] $x$TF2
INFO [2024-11-20 06:24:39] [1] 1 2 3
INFO [2024-11-20 06:24:39] 
INFO [2024-11-20 06:24:39] $x$TF3
INFO [2024-11-20 06:24:39] [1] 2 3 6
INFO [2024-11-20 06:24:39] 
INFO [2024-11-20 06:24:39] 
INFO [2024-11-20 06:24:39] $disable.logging
INFO [2024-11-20 06:24:39] [1] TRUE
INFO [2024-11-20 06:24:39] 
INFO [2024-11-20 06:24:39] $filename
INFO [2024-11-20 06:24:39] NULL
INFO [2024-11-20 06:24:39] 
INFO [2024-11-20 06:24:39] $scaled
INFO [2024-11-20 06:24:39] [1] FALSE
INFO [2024-11-20 06:24:39] 
INFO [2024-11-20 06:24:39] $euler.d
INFO [2024-11-20 06:24:39] [1] FALSE
INFO [2024-11-20 06:24:39] 
INFO [2024-11-20 06:24:39] $cat.cex
INFO [2024-11-20 06:24:39] [1] 1
INFO [2024-11-20 06:24:39] 
INFO [2024-11-20 06:24:39] $cat.col
INFO [2024-11-20 06:24:39] [1] "black"
INFO [2024-11-20 06:24:39] 
INFO [2024-11-20 06:24:39] $cat.fontface
INFO [2024-11-20 06:24:39] [1] "plain"
INFO [2024-11-20 06:24:39] 
INFO [2024-11-20 06:24:39] $cat.fontfamily
INFO [2024-11-20 06:24:39] [1] "serif"
INFO [2024-11-20 06:24:39] 
INFO [2024-11-20 06:24:39] $x
INFO [2024-11-20 06:24:39] $x$TF1
INFO [2024-11-20 06:24:39] [1] 3 4 5
INFO [2024-11-20 06:24:39] 
INFO [2024-11-20 06:24:39] $x$TF2
INFO [2024-11-20 06:24:39] [1] 1 2 5
INFO [2024-11-20 06:24:39] 
INFO [2024-11-20 06:24:39] $x$TF3
INFO [2024-11-20 06:24:39] [1] 1 2 5
INFO [2024-11-20 06:24:39] 
INFO [2024-11-20 06:24:39] 
INFO [2024-11-20 06:24:39] $disable.logging
INFO [2024-11-20 06:24:39] [1] TRUE
INFO [2024-11-20 06:24:39] 
INFO [2024-11-20 06:24:39] $filename
INFO [2024-11-20 06:24:39] NULL
INFO [2024-11-20 06:24:39] 
INFO [2024-11-20 06:24:40] $scaled
INFO [2024-11-20 06:24:40] [1] FALSE
INFO [2024-11-20 06:24:40] 
INFO [2024-11-20 06:24:40] $euler.d
INFO [2024-11-20 06:24:40] [1] FALSE
INFO [2024-11-20 06:24:40] 
INFO [2024-11-20 06:24:40] $cat.cex
INFO [2024-11-20 06:24:40] [1] 1
INFO [2024-11-20 06:24:40] 
INFO [2024-11-20 06:24:40] $cat.col
INFO [2024-11-20 06:24:40] [1] "black"
INFO [2024-11-20 06:24:40] 
INFO [2024-11-20 06:24:40] $cat.fontface
INFO [2024-11-20 06:24:40] [1] "plain"
INFO [2024-11-20 06:24:40] 
INFO [2024-11-20 06:24:40] $cat.fontfamily
INFO [2024-11-20 06:24:40] [1] "serif"
INFO [2024-11-20 06:24:40] 
INFO [2024-11-20 06:24:40] $x
INFO [2024-11-20 06:24:40] $x$TF1
INFO [2024-11-20 06:24:40] [1] 3 4 5
INFO [2024-11-20 06:24:40] 
INFO [2024-11-20 06:24:40] $x$TF2
INFO [2024-11-20 06:24:40] [1] 1 2 5
INFO [2024-11-20 06:24:40] 
INFO [2024-11-20 06:24:40] $x$TF3
INFO [2024-11-20 06:24:40] [1] 1 2 5
INFO [2024-11-20 06:24:40] 
INFO [2024-11-20 06:24:40] $x$TF4
INFO [2024-11-20 06:24:40] [1] 1 2 5
INFO [2024-11-20 06:24:40] 
INFO [2024-11-20 06:24:40] 
INFO [2024-11-20 06:24:40] $disable.logging
INFO [2024-11-20 06:24:40] [1] TRUE
INFO [2024-11-20 06:24:40] 
INFO [2024-11-20 06:24:40] $filename
INFO [2024-11-20 06:24:40] NULL
INFO [2024-11-20 06:24:40] 
[ 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 
232.378   3.341 263.999 

Example timings

ChIPpeakAnno.Rcheck/ChIPpeakAnno-Ex.timings

nameusersystemelapsed
ChIPpeakAnno-package0.0010.0000.000
ExonPlusUtr.human.GRCh373.9510.0884.047
HOT.spots0.1180.0040.122
IDRfilter0.0010.0000.000
Peaks.Ste12.Replicate10.0670.0000.067
Peaks.Ste12.Replicate20.0160.0000.017
Peaks.Ste12.Replicate30.0170.0000.017
TSS.human.GRCh370.2020.0000.202
TSS.human.GRCh380.1370.0000.138
TSS.human.NCBI360.1050.0000.105
TSS.mouse.GRCm380.0960.0040.100
TSS.mouse.NCBIM370.0860.0040.090
TSS.rat.RGSC3.40.0720.0080.080
TSS.rat.Rnor_5.00.0570.0080.064
TSS.zebrafish.Zv80.0690.0000.070
TSS.zebrafish.Zv90.0800.0040.085
addAncestors1.2660.0321.304
addGeneIDs1.0170.0201.043
addMetadata1.4000.0551.460
annoGR000
annoPeaks 3.872 0.31120.137
annotatePeakInBatch17.274 1.07818.389
annotatedPeak0.0550.0040.058
assignChromosomeRegion0.0010.0000.001
bdp000
binOverFeature0.9750.0481.026
binOverGene0.0000.0000.001
binOverRegions0.0000.0000.001
condenseMatrixByColnames0.0150.0000.015
convert2EntrezID0.5570.0120.569
countPatternInSeqs0.2070.0000.208
cumulativePercentage000
downstreams0.0320.0000.032
egOrgMap0.0010.0000.000
enrichedGO0.0030.0000.002
enrichmentPlot0.6750.0160.692
estFragmentLength0.0010.0000.000
estLibSize0.0010.0000.001
featureAlignedDistribution0.3200.0120.332
featureAlignedExtendSignal0.0020.0000.001
featureAlignedHeatmap0.4550.0160.471
featureAlignedSignal0.2430.0120.256
findEnhancers32.871 0.65833.598
findMotifsInPromoterSeqs19.407 0.18819.699
findOverlappingPeaks0.0010.0000.001
findOverlapsOfPeaks2.5200.0482.576
genomicElementDistribution0.0010.0000.001
genomicElementUpSetR0.0000.0000.001
getAllPeakSequence0.7030.0040.717
getAnnotation0.0010.0000.001
getEnrichedGO0.0100.0000.011
getEnrichedPATH0.0010.0000.001
getGO000
getGeneSeq0.0010.0000.001
getUniqueGOidCount0.0010.0000.001
getVennCounts0.0010.0000.001
hyperGtest0.0010.0000.001
makeVennDiagram0.0020.0000.003
mergePlusMinusPeaks0.0000.0000.001
metagenePlot2.7980.0522.859
myPeakList0.0140.0000.014
oligoFrequency0.1250.0000.125
oligoSummary0.0000.0000.001
peakPermTest0.0020.0000.002
peaks10.0060.0040.010
peaks20.0100.0000.011
peaks30.010.000.01
peaksNearBDP0.0010.0000.000
pie10.0060.0000.006
plotBinOverRegions0.0010.0000.000
preparePool0.0010.0000.000
reCenterPeaks0.0340.0000.034
summarizeOverlapsByBins6.6880.4776.841
summarizePatternInPeaks1.8740.2602.141
tileCount0.3750.3290.424
tileGRanges0.0420.0120.064
toGRanges0.0960.0280.125
translatePattern0.0010.0000.001
wgEncodeTfbsV30.1930.0080.202
write2FASTA0.0220.0000.023
xget0.1430.0160.160