| Back to Build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-05-31 05:44:31 -0000 (Wed, 31 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4219 |
| 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 | ||||
|
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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 323/2197 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ChIPpeakAnno 3.35.1 (landing page) Jianhong Ou
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: ChIPpeakAnno |
| Version: 3.35.1 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings ChIPpeakAnno_3.35.1.tar.gz |
| StartedAt: 2023-05-30 03:13:35 -0000 (Tue, 30 May 2023) |
| EndedAt: 2023-05-30 03:35:39 -0000 (Tue, 30 May 2023) |
| EllapsedTime: 1324.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ChIPpeakAnno.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings ChIPpeakAnno_3.35.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/ChIPpeakAnno.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘ChIPpeakAnno/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChIPpeakAnno’ version ‘3.35.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ChIPpeakAnno’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 19.1Mb
sub-directories of 1Mb or more:
data 12.6Mb
extdata 5.2Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘ensembldb’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) assignChromosomeRegion.Rd:133: Escaped LaTeX specials: \_
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
findEnhancers 33.849 0.548 34.399
findMotifsInPromoterSeqs 19.014 0.259 19.571
annotatePeakInBatch 16.338 0.568 16.907
summarizeOverlapsByBins 6.011 0.478 6.131
annoPeaks 4.389 0.315 10.824
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘ChIPpeakAnno.Rmd’ using ‘UTF-8’... OK
‘FAQs.Rmd’ using ‘UTF-8’... OK
‘pipeline.Rmd’ using ‘UTF-8’... OK
‘quickStart.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/home/biocbuild/bbs-3.18-bioc/meat/ChIPpeakAnno.Rcheck/00check.log’
for details.
ChIPpeakAnno.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL ChIPpeakAnno ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/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 in method for ‘annoGR’ with signature ‘"EnsDb"’: no definition for class “EnsDb” in method for ‘toGRanges’ with signature ‘"EnsDb"’: no definition for class “EnsDb” ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ChIPpeakAnno)
ChIPpeakAnno.Rcheck/tests/runTests.Rout
R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> require("ChIPpeakAnno") || stop("unable to load Package:ChIPpeakAnno")
Loading required package: ChIPpeakAnno
Loading required package: IRanges
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
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: rtracklayer
[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 [2023-05-30 03:26:17] $cat.cex
INFO [2023-05-30 03:26:17] [1] 1
INFO [2023-05-30 03:26:17]
INFO [2023-05-30 03:26:17] $cat.col
INFO [2023-05-30 03:26:17] [1] "black"
INFO [2023-05-30 03:26:17]
INFO [2023-05-30 03:26:17] $cat.fontface
INFO [2023-05-30 03:26:17] [1] "plain"
INFO [2023-05-30 03:26:17]
INFO [2023-05-30 03:26:17] $cat.fontfamily
INFO [2023-05-30 03:26:17] [1] "serif"
INFO [2023-05-30 03:26:17]
INFO [2023-05-30 03:26:17] $x
INFO [2023-05-30 03:26:17] $x$TF1
INFO [2023-05-30 03:26:17] [1] 3 4 5
INFO [2023-05-30 03:26:17]
INFO [2023-05-30 03:26:17] $x$TF2
INFO [2023-05-30 03:26:17] [1] 1 2 3 4 5
INFO [2023-05-30 03:26:17]
INFO [2023-05-30 03:26:17]
INFO [2023-05-30 03:26:17] $filename
INFO [2023-05-30 03:26:17] NULL
INFO [2023-05-30 03:26:17]
INFO [2023-05-30 03:26:17] $disable.logging
INFO [2023-05-30 03:26:17] [1] TRUE
INFO [2023-05-30 03:26:17]
INFO [2023-05-30 03:26:17] $cat.cex
INFO [2023-05-30 03:26:17] [1] 1
INFO [2023-05-30 03:26:17]
INFO [2023-05-30 03:26:17] $cat.col
INFO [2023-05-30 03:26:17] [1] "black"
INFO [2023-05-30 03:26:17]
INFO [2023-05-30 03:26:17] $cat.fontface
INFO [2023-05-30 03:26:17] [1] "plain"
INFO [2023-05-30 03:26:17]
INFO [2023-05-30 03:26:17] $cat.fontfamily
INFO [2023-05-30 03:26:17] [1] "serif"
INFO [2023-05-30 03:26:17]
INFO [2023-05-30 03:26:17] $x
INFO [2023-05-30 03:26:17] $x$TF1
INFO [2023-05-30 03:26:17] [1] 3 4 5
INFO [2023-05-30 03:26:17]
INFO [2023-05-30 03:26:17] $x$TF2
INFO [2023-05-30 03:26:17] [1] 1 2 4 5
INFO [2023-05-30 03:26:17]
INFO [2023-05-30 03:26:17] $x$TF3
INFO [2023-05-30 03:26:17] [1] 3 4 5
INFO [2023-05-30 03:26:17]
INFO [2023-05-30 03:26:17] $x$TF4
INFO [2023-05-30 03:26:17] [1] 1 2 4 5
INFO [2023-05-30 03:26:17]
INFO [2023-05-30 03:26:17]
INFO [2023-05-30 03:26:17] $filename
INFO [2023-05-30 03:26:17] NULL
INFO [2023-05-30 03:26:17]
INFO [2023-05-30 03:26:17] $disable.logging
INFO [2023-05-30 03:26:17] [1] TRUE
INFO [2023-05-30 03:26:17]
INFO [2023-05-30 03:26:18] $scaled
INFO [2023-05-30 03:26:18] [1] FALSE
INFO [2023-05-30 03:26:18]
INFO [2023-05-30 03:26:18] $euler.d
INFO [2023-05-30 03:26:18] [1] FALSE
INFO [2023-05-30 03:26:18]
INFO [2023-05-30 03:26:18] $cat.cex
INFO [2023-05-30 03:26:18] [1] 1
INFO [2023-05-30 03:26:18]
INFO [2023-05-30 03:26:18] $cat.col
INFO [2023-05-30 03:26:18] [1] "black"
INFO [2023-05-30 03:26:18]
INFO [2023-05-30 03:26:18] $cat.fontface
INFO [2023-05-30 03:26:18] [1] "plain"
INFO [2023-05-30 03:26:18]
INFO [2023-05-30 03:26:18] $cat.fontfamily
INFO [2023-05-30 03:26:18] [1] "serif"
INFO [2023-05-30 03:26:18]
INFO [2023-05-30 03:26:18] $x
INFO [2023-05-30 03:26:18] $x$TF1
INFO [2023-05-30 03:26:18] [1] 1 2 3
INFO [2023-05-30 03:26:18]
INFO [2023-05-30 03:26:18] $x$TF2
INFO [2023-05-30 03:26:18] [1] 1 2 3
INFO [2023-05-30 03:26:18]
INFO [2023-05-30 03:26:18]
INFO [2023-05-30 03:26:18] $filename
INFO [2023-05-30 03:26:18] NULL
INFO [2023-05-30 03:26:18]
INFO [2023-05-30 03:26:18] $disable.logging
INFO [2023-05-30 03:26:18] [1] TRUE
INFO [2023-05-30 03:26:18]
INFO [2023-05-30 03:26:18] $scaled
INFO [2023-05-30 03:26:18] [1] FALSE
INFO [2023-05-30 03:26:18]
INFO [2023-05-30 03:26:18] $euler.d
INFO [2023-05-30 03:26:18] [1] FALSE
INFO [2023-05-30 03:26:18]
INFO [2023-05-30 03:26:18] $cat.cex
INFO [2023-05-30 03:26:18] [1] 1
INFO [2023-05-30 03:26:18]
INFO [2023-05-30 03:26:18] $cat.col
INFO [2023-05-30 03:26:18] [1] "black"
INFO [2023-05-30 03:26:18]
INFO [2023-05-30 03:26:18] $cat.fontface
INFO [2023-05-30 03:26:18] [1] "plain"
INFO [2023-05-30 03:26:18]
INFO [2023-05-30 03:26:18] $cat.fontfamily
INFO [2023-05-30 03:26:18] [1] "serif"
INFO [2023-05-30 03:26:18]
INFO [2023-05-30 03:26:18] $x
INFO [2023-05-30 03:26:18] $x$TF1
INFO [2023-05-30 03:26:18] [1] 4 5 6
INFO [2023-05-30 03:26:18]
INFO [2023-05-30 03:26:18] $x$TF2
INFO [2023-05-30 03:26:18] [1] 1 2 3
INFO [2023-05-30 03:26:18]
INFO [2023-05-30 03:26:18]
INFO [2023-05-30 03:26:18] $filename
INFO [2023-05-30 03:26:18] NULL
INFO [2023-05-30 03:26:18]
INFO [2023-05-30 03:26:18] $disable.logging
INFO [2023-05-30 03:26:18] [1] TRUE
INFO [2023-05-30 03:26:18]
INFO [2023-05-30 03:26:19] $scaled
INFO [2023-05-30 03:26:19] [1] FALSE
INFO [2023-05-30 03:26:19]
INFO [2023-05-30 03:26:19] $euler.d
INFO [2023-05-30 03:26:19] [1] FALSE
INFO [2023-05-30 03:26:19]
INFO [2023-05-30 03:26:19] $cat.cex
INFO [2023-05-30 03:26:19] [1] 1
INFO [2023-05-30 03:26:19]
INFO [2023-05-30 03:26:19] $cat.col
INFO [2023-05-30 03:26:19] [1] "black"
INFO [2023-05-30 03:26:19]
INFO [2023-05-30 03:26:19] $cat.fontface
INFO [2023-05-30 03:26:19] [1] "plain"
INFO [2023-05-30 03:26:19]
INFO [2023-05-30 03:26:19] $cat.fontfamily
INFO [2023-05-30 03:26:19] [1] "serif"
INFO [2023-05-30 03:26:19]
INFO [2023-05-30 03:26:19] $x
INFO [2023-05-30 03:26:19] $x$TF1
INFO [2023-05-30 03:26:19] [1] 4 5 6
INFO [2023-05-30 03:26:19]
INFO [2023-05-30 03:26:19] $x$TF2
INFO [2023-05-30 03:26:19] [1] 1 2 3
INFO [2023-05-30 03:26:19]
INFO [2023-05-30 03:26:19]
INFO [2023-05-30 03:26:19] $filename
INFO [2023-05-30 03:26:19] NULL
INFO [2023-05-30 03:26:19]
INFO [2023-05-30 03:26:19] $disable.logging
INFO [2023-05-30 03:26:19] [1] TRUE
INFO [2023-05-30 03:26:19]
INFO [2023-05-30 03:26:19] $scaled
INFO [2023-05-30 03:26:19] [1] FALSE
INFO [2023-05-30 03:26:19]
INFO [2023-05-30 03:26:19] $euler.d
INFO [2023-05-30 03:26:19] [1] FALSE
INFO [2023-05-30 03:26:19]
INFO [2023-05-30 03:26:19] $cat.cex
INFO [2023-05-30 03:26:19] [1] 1
INFO [2023-05-30 03:26:19]
INFO [2023-05-30 03:26:19] $cat.col
INFO [2023-05-30 03:26:19] [1] "black"
INFO [2023-05-30 03:26:19]
INFO [2023-05-30 03:26:19] $cat.fontface
INFO [2023-05-30 03:26:19] [1] "plain"
INFO [2023-05-30 03:26:19]
INFO [2023-05-30 03:26:19] $cat.fontfamily
INFO [2023-05-30 03:26:19] [1] "serif"
INFO [2023-05-30 03:26:19]
INFO [2023-05-30 03:26:19] $x
INFO [2023-05-30 03:26:19] $x$TF1
INFO [2023-05-30 03:26:19] [1] 4 5 6
INFO [2023-05-30 03:26:19]
INFO [2023-05-30 03:26:19] $x$TF2
INFO [2023-05-30 03:26:19] [1] 1 2 3
INFO [2023-05-30 03:26:19]
INFO [2023-05-30 03:26:19] $x$TF3
INFO [2023-05-30 03:26:19] [1] 2 3 6
INFO [2023-05-30 03:26:19]
INFO [2023-05-30 03:26:19]
INFO [2023-05-30 03:26:19] $filename
INFO [2023-05-30 03:26:19] NULL
INFO [2023-05-30 03:26:19]
INFO [2023-05-30 03:26:19] $disable.logging
INFO [2023-05-30 03:26:19] [1] TRUE
INFO [2023-05-30 03:26:19]
INFO [2023-05-30 03:26:19] $scaled
INFO [2023-05-30 03:26:19] [1] FALSE
INFO [2023-05-30 03:26:19]
INFO [2023-05-30 03:26:19] $euler.d
INFO [2023-05-30 03:26:19] [1] FALSE
INFO [2023-05-30 03:26:19]
INFO [2023-05-30 03:26:19] $cat.cex
INFO [2023-05-30 03:26:19] [1] 1
INFO [2023-05-30 03:26:19]
INFO [2023-05-30 03:26:19] $cat.col
INFO [2023-05-30 03:26:19] [1] "black"
INFO [2023-05-30 03:26:19]
INFO [2023-05-30 03:26:19] $cat.fontface
INFO [2023-05-30 03:26:19] [1] "plain"
INFO [2023-05-30 03:26:19]
INFO [2023-05-30 03:26:19] $cat.fontfamily
INFO [2023-05-30 03:26:19] [1] "serif"
INFO [2023-05-30 03:26:19]
INFO [2023-05-30 03:26:19] $x
INFO [2023-05-30 03:26:19] $x$TF1
INFO [2023-05-30 03:26:19] [1] 3 4 5
INFO [2023-05-30 03:26:19]
INFO [2023-05-30 03:26:19] $x$TF2
INFO [2023-05-30 03:26:19] [1] 1 2 5
INFO [2023-05-30 03:26:19]
INFO [2023-05-30 03:26:19] $x$TF3
INFO [2023-05-30 03:26:19] [1] 1 2 5
INFO [2023-05-30 03:26:19]
INFO [2023-05-30 03:26:19]
INFO [2023-05-30 03:26:19] $filename
INFO [2023-05-30 03:26:19] NULL
INFO [2023-05-30 03:26:19]
INFO [2023-05-30 03:26:19] $disable.logging
INFO [2023-05-30 03:26:19] [1] TRUE
INFO [2023-05-30 03:26:19]
INFO [2023-05-30 03:26:20] $scaled
INFO [2023-05-30 03:26:20] [1] FALSE
INFO [2023-05-30 03:26:20]
INFO [2023-05-30 03:26:20] $euler.d
INFO [2023-05-30 03:26:20] [1] FALSE
INFO [2023-05-30 03:26:20]
INFO [2023-05-30 03:26:20] $cat.cex
INFO [2023-05-30 03:26:20] [1] 1
INFO [2023-05-30 03:26:20]
INFO [2023-05-30 03:26:20] $cat.col
INFO [2023-05-30 03:26:20] [1] "black"
INFO [2023-05-30 03:26:20]
INFO [2023-05-30 03:26:20] $cat.fontface
INFO [2023-05-30 03:26:20] [1] "plain"
INFO [2023-05-30 03:26:20]
INFO [2023-05-30 03:26:20] $cat.fontfamily
INFO [2023-05-30 03:26:20] [1] "serif"
INFO [2023-05-30 03:26:20]
INFO [2023-05-30 03:26:20] $x
INFO [2023-05-30 03:26:20] $x$TF1
INFO [2023-05-30 03:26:20] [1] 3 4 5
INFO [2023-05-30 03:26:20]
INFO [2023-05-30 03:26:20] $x$TF2
INFO [2023-05-30 03:26:20] [1] 1 2 5
INFO [2023-05-30 03:26:20]
INFO [2023-05-30 03:26:20] $x$TF3
INFO [2023-05-30 03:26:20] [1] 1 2 5
INFO [2023-05-30 03:26:20]
INFO [2023-05-30 03:26:20] $x$TF4
INFO [2023-05-30 03:26:20] [1] 1 2 5
INFO [2023-05-30 03:26:20]
INFO [2023-05-30 03:26:20]
INFO [2023-05-30 03:26:20] $filename
INFO [2023-05-30 03:26:20] NULL
INFO [2023-05-30 03:26:20]
INFO [2023-05-30 03:26:20] $disable.logging
INFO [2023-05-30 03:26:20] [1] TRUE
INFO [2023-05-30 03:26:20]
[ FAIL 0 | WARN 4 | SKIP 6 | PASS 316 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (6)
[ FAIL 0 | WARN 4 | SKIP 6 | PASS 316 ]
>
> proc.time()
user system elapsed
223.339 4.670 243.068
ChIPpeakAnno.Rcheck/ChIPpeakAnno-Ex.timings
| name | user | system | elapsed | |
| ChIPpeakAnno-package | 0.001 | 0.000 | 0.000 | |
| ExonPlusUtr.human.GRCh37 | 3.484 | 0.172 | 3.656 | |
| HOT.spots | 0.111 | 0.016 | 0.127 | |
| IDRfilter | 0.001 | 0.000 | 0.001 | |
| Peaks.Ste12.Replicate1 | 0.059 | 0.004 | 0.062 | |
| Peaks.Ste12.Replicate2 | 0.015 | 0.001 | 0.015 | |
| Peaks.Ste12.Replicate3 | 0.015 | 0.000 | 0.015 | |
| TSS.human.GRCh37 | 0.193 | 0.012 | 0.205 | |
| TSS.human.GRCh38 | 0.129 | 0.007 | 0.137 | |
| TSS.human.NCBI36 | 0.105 | 0.001 | 0.105 | |
| TSS.mouse.GRCm38 | 0.093 | 0.011 | 0.106 | |
| TSS.mouse.NCBIM37 | 0.078 | 0.013 | 0.090 | |
| TSS.rat.RGSC3.4 | 0.071 | 0.004 | 0.075 | |
| TSS.rat.Rnor_5.0 | 0.066 | 0.000 | 0.066 | |
| TSS.zebrafish.Zv8 | 0.066 | 0.003 | 0.070 | |
| TSS.zebrafish.Zv9 | 0.072 | 0.012 | 0.084 | |
| addAncestors | 1.347 | 0.031 | 1.379 | |
| addGeneIDs | 0.982 | 0.045 | 1.028 | |
| addMetadata | 1.320 | 0.124 | 1.445 | |
| annoGR | 0.001 | 0.000 | 0.000 | |
| annoPeaks | 4.389 | 0.315 | 10.824 | |
| annotatePeakInBatch | 16.338 | 0.568 | 16.907 | |
| annotatedPeak | 0.055 | 0.004 | 0.059 | |
| assignChromosomeRegion | 0.001 | 0.000 | 0.001 | |
| bdp | 0 | 0 | 0 | |
| binOverFeature | 0.936 | 0.017 | 0.954 | |
| binOverGene | 0.000 | 0.000 | 0.001 | |
| binOverRegions | 0 | 0 | 0 | |
| condenseMatrixByColnames | 0.014 | 0.000 | 0.014 | |
| convert2EntrezID | 0.440 | 0.003 | 0.443 | |
| countPatternInSeqs | 0.208 | 0.016 | 0.225 | |
| cumulativePercentage | 0 | 0 | 0 | |
| downstreams | 0.118 | 0.000 | 0.118 | |
| egOrgMap | 0.001 | 0.000 | 0.001 | |
| enrichedGO | 0.002 | 0.000 | 0.003 | |
| enrichmentPlot | 0.662 | 0.020 | 0.682 | |
| estFragmentLength | 0.000 | 0.000 | 0.001 | |
| estLibSize | 0.000 | 0.000 | 0.001 | |
| featureAlignedDistribution | 0.284 | 0.003 | 0.287 | |
| featureAlignedExtendSignal | 0.001 | 0.000 | 0.001 | |
| featureAlignedHeatmap | 0.419 | 0.000 | 0.419 | |
| featureAlignedSignal | 0.240 | 0.024 | 0.264 | |
| findEnhancers | 33.849 | 0.548 | 34.399 | |
| findMotifsInPromoterSeqs | 19.014 | 0.259 | 19.571 | |
| findOverlappingPeaks | 0.001 | 0.000 | 0.001 | |
| findOverlapsOfPeaks | 2.453 | 0.020 | 2.473 | |
| genomicElementDistribution | 0.001 | 0.000 | 0.001 | |
| genomicElementUpSetR | 0.001 | 0.000 | 0.000 | |
| getAllPeakSequence | 0.626 | 0.036 | 0.663 | |
| getAnnotation | 0.001 | 0.000 | 0.001 | |
| getEnrichedGO | 0.012 | 0.000 | 0.012 | |
| getEnrichedPATH | 0.001 | 0.000 | 0.000 | |
| getGO | 0 | 0 | 0 | |
| getGeneSeq | 0.001 | 0.000 | 0.001 | |
| getUniqueGOidCount | 0.001 | 0.000 | 0.001 | |
| getVennCounts | 0.001 | 0.000 | 0.001 | |
| hyperGtest | 0.001 | 0.000 | 0.001 | |
| makeVennDiagram | 0.003 | 0.000 | 0.002 | |
| mergePlusMinusPeaks | 0 | 0 | 0 | |
| metagenePlot | 2.654 | 0.072 | 2.729 | |
| myPeakList | 0.015 | 0.000 | 0.015 | |
| oligoFrequency | 0.211 | 0.004 | 0.215 | |
| oligoSummary | 0 | 0 | 0 | |
| peakPermTest | 0.002 | 0.000 | 0.002 | |
| peaksNearBDP | 0.001 | 0.000 | 0.000 | |
| pie1 | 0.006 | 0.000 | 0.006 | |
| plotBinOverRegions | 0 | 0 | 0 | |
| preparePool | 0 | 0 | 0 | |
| reCenterPeaks | 0.033 | 0.000 | 0.033 | |
| summarizeOverlapsByBins | 6.011 | 0.478 | 6.131 | |
| summarizePatternInPeaks | 0.668 | 0.048 | 0.716 | |
| tileCount | 0.268 | 0.209 | 0.411 | |
| tileGRanges | 0.169 | 0.148 | 0.052 | |
| toGRanges | 0.102 | 0.016 | 0.118 | |
| translatePattern | 0.001 | 0.000 | 0.001 | |
| wgEncodeTfbsV3 | 0.191 | 0.008 | 0.199 | |
| write2FASTA | 0.022 | 0.004 | 0.025 | |
| xget | 0.119 | 0.020 | 0.140 | |