Jianhong Ou
| Snapshot Date: 2024-05-29 14:00:10 -0400 (Wed, 29 May 2024) |
| git_url: https://git.bioconductor.org/packages/ChIPpeakAnno |
| git_branch: RELEASE_3_19 |
| git_last_commit: 26e03e3 |
| git_last_commit_date: 2024-04-30 10:20:21 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-30 11:35:28 -0400 (Thu, 30 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4753 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4518 |
| 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 337/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ChIPpeakAnno 3.38.0 (landing page) Jianhong Ou
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
|
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. |
| Package: ChIPpeakAnno |
| Version: 3.38.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ChIPpeakAnno_3.38.0.tar.gz |
| StartedAt: 2024-05-29 19:43:17 -0400 (Wed, 29 May 2024) |
| EndedAt: 2024-05-29 19:55:30 -0400 (Wed, 29 May 2024) |
| EllapsedTime: 733.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ChIPpeakAnno.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ChIPpeakAnno_3.38.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/ChIPpeakAnno.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChIPpeakAnno/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChIPpeakAnno’ version ‘3.38.0’
* 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 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 ... NOTE
checkRd: (-1) summarizePatternInPeaks.Rd:63: Lost braces; missing escapes or markup?
63 | {shuffle_sequences}}
| ^
checkRd: (-1) summarizePatternInPeaks.Rd:69: Lost braces; missing escapes or markup?
69 | \item{"patternNum"}: {number of matched pattern}
| ^
checkRd: (-1) summarizePatternInPeaks.Rd:70-71: Lost braces
70 | \item{"totalNumPatternWithSameLen"}: {total number of pattern with the
| ^
checkRd: (-1) summarizePatternInPeaks.Rd:72: Lost braces; missing escapes or markup?
72 | \item{"expectedRate"}: {expected rate of pattern for 'binom.test' method}
| ^
checkRd: (-1) summarizePatternInPeaks.Rd:73: Lost braces; missing escapes or markup?
73 | \item{"patternRate"}: {real rate of pattern for 'permutation.test' method}
| ^
checkRd: (-1) summarizePatternInPeaks.Rd:74: Lost braces; missing escapes or markup?
74 | \item{"pValueBinomTest"}: {p value of bimom test for 'binom.test' method}
| ^
checkRd: (-1) summarizePatternInPeaks.Rd:75-76: Lost braces
75 | \item{"cutOffPermutationTest"}: {cut off of permutation test for
| ^
checkRd: (-1) summarizePatternInPeaks.Rd:82: Lost braces; missing escapes or markup?
82 | \item{"motifChr"}: {Chromosome of motif}
| ^
checkRd: (-1) summarizePatternInPeaks.Rd:83: Lost braces; missing escapes or markup?
83 | \item{"motifStartInChr"}: {motif start position in chromosome}
| ^
checkRd: (-1) summarizePatternInPeaks.Rd:84: Lost braces; missing escapes or markup?
84 | \item{"motifEndInChr"}: {motif end position in chromosome}
| ^
checkRd: (-1) summarizePatternInPeaks.Rd:85: Lost braces; missing escapes or markup?
85 | \item{"motifName"}: {motif name}
| ^
checkRd: (-1) summarizePatternInPeaks.Rd:86: Lost braces; missing escapes or markup?
86 | \item{"motifPattern"}: {motif pattern}
| ^
checkRd: (-1) summarizePatternInPeaks.Rd:87: Lost braces; missing escapes or markup?
87 | \item{"motifStartInPeak"}: {motif start position in peak}
| ^
checkRd: (-1) summarizePatternInPeaks.Rd:88: Lost braces; missing escapes or markup?
88 | \item{"motifEndInPeak"}: {motif end position in peak}
| ^
checkRd: (-1) summarizePatternInPeaks.Rd:89: Lost braces; missing escapes or markup?
89 | \item{"motifFound"}: {specific motif Found in peak}
| ^
checkRd: (-1) summarizePatternInPeaks.Rd:90-91: Lost braces
90 | \item{"motifFoundStrand"}: {strand of specific motif Found in peak, "-"
| ^
checkRd: (-1) summarizePatternInPeaks.Rd:92: Lost braces; missing escapes or markup?
92 | \item{"peakChr"}: {Chromosome of peak}
| ^
checkRd: (-1) summarizePatternInPeaks.Rd:93: Lost braces; missing escapes or markup?
93 | \item{"peakStart"}: {peak start position}
| ^
checkRd: (-1) summarizePatternInPeaks.Rd:94: Lost braces; missing escapes or markup?
94 | \item{"peakEnd"}: {peak end position}
| ^
checkRd: (-1) summarizePatternInPeaks.Rd:95: Lost braces; missing escapes or markup?
95 | \item{"peakWidth"}: {peak width}
| ^
checkRd: (-1) summarizePatternInPeaks.Rd:96: Lost braces; missing escapes or markup?
96 | \item{"peakStrand"}: {peak strand}
| ^
* 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 30.968 1.261 32.837
findMotifsInPromoterSeqs 18.826 0.586 19.968
annotatePeakInBatch 15.102 0.898 16.215
summarizeOverlapsByBins 5.803 0.610 6.169
* 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.19-bioc/meat/ChIPpeakAnno.Rcheck/00check.log’
for details.
ChIPpeakAnno.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ChIPpeakAnno ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘ChIPpeakAnno’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ChIPpeakAnno)
ChIPpeakAnno.Rcheck/tests/runTests.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> require("ChIPpeakAnno") || stop("unable to load Package:ChIPpeakAnno")
Loading required package: ChIPpeakAnno
Loading required package: IRanges
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
[1] TRUE
> require("BSgenome.Drerio.UCSC.danRer7") || stop("unable to load Package:BSgenome.Drerio.UCSC.danRer7")
Loading required package: BSgenome.Drerio.UCSC.danRer7
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: BiocIO
Loading required package: rtracklayer
Attaching package: 'rtracklayer'
The following object is masked from 'package:BiocIO':
FileForFormat
[1] TRUE
> require("BSgenome.Hsapiens.UCSC.hg19") || stop("unable to load Package:BSgenome.Hsapiens.UCSC.hg19")
Loading required package: BSgenome.Hsapiens.UCSC.hg19
[1] TRUE
> require("org.Hs.eg.db") || stop("unable to load Package:org.Hs.eg.db")
Loading required package: org.Hs.eg.db
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
[1] TRUE
> require("org.Ce.eg.db") || stop("unable to load Package:org.Ce.eg.db")
Loading required package: org.Ce.eg.db
[1] TRUE
> require("BSgenome.Celegans.UCSC.ce10") || stop("unable to load Package:BSgenome.Celegans.UCSC.ce10")
Loading required package: BSgenome.Celegans.UCSC.ce10
[1] TRUE
> require("EnsDb.Hsapiens.v79") || stop("unable to load Package:EnsDb.Hsapiens.v79")
Loading required package: EnsDb.Hsapiens.v79
Loading required package: ensembldb
Loading required package: GenomicFeatures
Loading required package: AnnotationFilter
Attaching package: 'ensembldb'
The following object is masked from 'package:stats':
filter
[1] TRUE
> require("TxDb.Hsapiens.UCSC.hg38.knownGene") || stop("unable to load TxDb.Hsapiens.UCSC.hg38.knownGene")
Loading required package: TxDb.Hsapiens.UCSC.hg38.knownGene
[1] TRUE
> require("biomaRt") || stop("unable to load biomaRt")
Loading required package: biomaRt
[1] TRUE
> require("reactome.db") || stop("unable to load reactome.db")
Loading required package: reactome.db
[1] TRUE
> require("testthat") || stop("unable to load testthat")
Loading required package: testthat
Attaching package: 'testthat'
The following object is masked from 'package:AnnotationFilter':
not
[1] TRUE
> test_check("ChIPpeakAnno")
INFO [2024-05-29 19:55:03] $cat.cex
INFO [2024-05-29 19:55:03] [1] 1
INFO [2024-05-29 19:55:03]
INFO [2024-05-29 19:55:03] $cat.col
INFO [2024-05-29 19:55:03] [1] "black"
INFO [2024-05-29 19:55:03]
INFO [2024-05-29 19:55:03] $cat.fontface
INFO [2024-05-29 19:55:03] [1] "plain"
INFO [2024-05-29 19:55:03]
INFO [2024-05-29 19:55:03] $cat.fontfamily
INFO [2024-05-29 19:55:03] [1] "serif"
INFO [2024-05-29 19:55:03]
INFO [2024-05-29 19:55:03] $x
INFO [2024-05-29 19:55:03] $x$TF1
INFO [2024-05-29 19:55:03] [1] 3 4 5
INFO [2024-05-29 19:55:03]
INFO [2024-05-29 19:55:03] $x$TF2
INFO [2024-05-29 19:55:03] [1] 1 2 3 4 5
INFO [2024-05-29 19:55:03]
INFO [2024-05-29 19:55:03]
INFO [2024-05-29 19:55:03] $disable.logging
INFO [2024-05-29 19:55:03] [1] TRUE
INFO [2024-05-29 19:55:03]
INFO [2024-05-29 19:55:03] $filename
INFO [2024-05-29 19:55:03] NULL
INFO [2024-05-29 19:55:03]
INFO [2024-05-29 19:55:04] $cat.cex
INFO [2024-05-29 19:55:04] [1] 1
INFO [2024-05-29 19:55:04]
INFO [2024-05-29 19:55:04] $cat.col
INFO [2024-05-29 19:55:04] [1] "black"
INFO [2024-05-29 19:55:04]
INFO [2024-05-29 19:55:04] $cat.fontface
INFO [2024-05-29 19:55:04] [1] "plain"
INFO [2024-05-29 19:55:04]
INFO [2024-05-29 19:55:04] $cat.fontfamily
INFO [2024-05-29 19:55:04] [1] "serif"
INFO [2024-05-29 19:55:04]
INFO [2024-05-29 19:55:04] $x
INFO [2024-05-29 19:55:04] $x$TF1
INFO [2024-05-29 19:55:04] [1] 3 4 5
INFO [2024-05-29 19:55:04]
INFO [2024-05-29 19:55:04] $x$TF2
INFO [2024-05-29 19:55:04] [1] 1 2 4 5
INFO [2024-05-29 19:55:04]
INFO [2024-05-29 19:55:04] $x$TF3
INFO [2024-05-29 19:55:04] [1] 3 4 5
INFO [2024-05-29 19:55:04]
INFO [2024-05-29 19:55:04] $x$TF4
INFO [2024-05-29 19:55:04] [1] 1 2 4 5
INFO [2024-05-29 19:55:04]
INFO [2024-05-29 19:55:04]
INFO [2024-05-29 19:55:04] $disable.logging
INFO [2024-05-29 19:55:04] [1] TRUE
INFO [2024-05-29 19:55:04]
INFO [2024-05-29 19:55:04] $filename
INFO [2024-05-29 19:55:04] NULL
INFO [2024-05-29 19:55:04]
INFO [2024-05-29 19:55:04] $scaled
INFO [2024-05-29 19:55:04] [1] FALSE
INFO [2024-05-29 19:55:04]
INFO [2024-05-29 19:55:04] $euler.d
INFO [2024-05-29 19:55:04] [1] FALSE
INFO [2024-05-29 19:55:04]
INFO [2024-05-29 19:55:04] $cat.cex
INFO [2024-05-29 19:55:04] [1] 1
INFO [2024-05-29 19:55:04]
INFO [2024-05-29 19:55:04] $cat.col
INFO [2024-05-29 19:55:04] [1] "black"
INFO [2024-05-29 19:55:04]
INFO [2024-05-29 19:55:04] $cat.fontface
INFO [2024-05-29 19:55:04] [1] "plain"
INFO [2024-05-29 19:55:04]
INFO [2024-05-29 19:55:04] $cat.fontfamily
INFO [2024-05-29 19:55:04] [1] "serif"
INFO [2024-05-29 19:55:04]
INFO [2024-05-29 19:55:04] $x
INFO [2024-05-29 19:55:04] $x$TF1
INFO [2024-05-29 19:55:04] [1] 1 2 3
INFO [2024-05-29 19:55:04]
INFO [2024-05-29 19:55:04] $x$TF2
INFO [2024-05-29 19:55:04] [1] 1 2 3
INFO [2024-05-29 19:55:04]
INFO [2024-05-29 19:55:04]
INFO [2024-05-29 19:55:04] $disable.logging
INFO [2024-05-29 19:55:04] [1] TRUE
INFO [2024-05-29 19:55:04]
INFO [2024-05-29 19:55:04] $filename
INFO [2024-05-29 19:55:04] NULL
INFO [2024-05-29 19:55:04]
INFO [2024-05-29 19:55:04] $scaled
INFO [2024-05-29 19:55:04] [1] FALSE
INFO [2024-05-29 19:55:04]
INFO [2024-05-29 19:55:04] $euler.d
INFO [2024-05-29 19:55:04] [1] FALSE
INFO [2024-05-29 19:55:04]
INFO [2024-05-29 19:55:04] $cat.cex
INFO [2024-05-29 19:55:04] [1] 1
INFO [2024-05-29 19:55:04]
INFO [2024-05-29 19:55:04] $cat.col
INFO [2024-05-29 19:55:04] [1] "black"
INFO [2024-05-29 19:55:04]
INFO [2024-05-29 19:55:04] $cat.fontface
INFO [2024-05-29 19:55:04] [1] "plain"
INFO [2024-05-29 19:55:04]
INFO [2024-05-29 19:55:04] $cat.fontfamily
INFO [2024-05-29 19:55:04] [1] "serif"
INFO [2024-05-29 19:55:04]
INFO [2024-05-29 19:55:04] $x
INFO [2024-05-29 19:55:04] $x$TF1
INFO [2024-05-29 19:55:04] [1] 4 5 6
INFO [2024-05-29 19:55:04]
INFO [2024-05-29 19:55:04] $x$TF2
INFO [2024-05-29 19:55:04] [1] 1 2 3
INFO [2024-05-29 19:55:04]
INFO [2024-05-29 19:55:04]
INFO [2024-05-29 19:55:04] $disable.logging
INFO [2024-05-29 19:55:04] [1] TRUE
INFO [2024-05-29 19:55:04]
INFO [2024-05-29 19:55:04] $filename
INFO [2024-05-29 19:55:04] NULL
INFO [2024-05-29 19:55:04]
INFO [2024-05-29 19:55:05] $scaled
INFO [2024-05-29 19:55:05] [1] FALSE
INFO [2024-05-29 19:55:05]
INFO [2024-05-29 19:55:05] $euler.d
INFO [2024-05-29 19:55:05] [1] FALSE
INFO [2024-05-29 19:55:05]
INFO [2024-05-29 19:55:05] $cat.cex
INFO [2024-05-29 19:55:05] [1] 1
INFO [2024-05-29 19:55:05]
INFO [2024-05-29 19:55:05] $cat.col
INFO [2024-05-29 19:55:05] [1] "black"
INFO [2024-05-29 19:55:05]
INFO [2024-05-29 19:55:05] $cat.fontface
INFO [2024-05-29 19:55:05] [1] "plain"
INFO [2024-05-29 19:55:05]
INFO [2024-05-29 19:55:05] $cat.fontfamily
INFO [2024-05-29 19:55:05] [1] "serif"
INFO [2024-05-29 19:55:05]
INFO [2024-05-29 19:55:05] $x
INFO [2024-05-29 19:55:05] $x$TF1
INFO [2024-05-29 19:55:05] [1] 4 5 6
INFO [2024-05-29 19:55:05]
INFO [2024-05-29 19:55:05] $x$TF2
INFO [2024-05-29 19:55:05] [1] 1 2 3
INFO [2024-05-29 19:55:05]
INFO [2024-05-29 19:55:05]
INFO [2024-05-29 19:55:05] $disable.logging
INFO [2024-05-29 19:55:05] [1] TRUE
INFO [2024-05-29 19:55:05]
INFO [2024-05-29 19:55:05] $filename
INFO [2024-05-29 19:55:05] NULL
INFO [2024-05-29 19:55:05]
INFO [2024-05-29 19:55:05] $scaled
INFO [2024-05-29 19:55:05] [1] FALSE
INFO [2024-05-29 19:55:05]
INFO [2024-05-29 19:55:05] $euler.d
INFO [2024-05-29 19:55:05] [1] FALSE
INFO [2024-05-29 19:55:05]
INFO [2024-05-29 19:55:05] $cat.cex
INFO [2024-05-29 19:55:05] [1] 1
INFO [2024-05-29 19:55:05]
INFO [2024-05-29 19:55:05] $cat.col
INFO [2024-05-29 19:55:05] [1] "black"
INFO [2024-05-29 19:55:05]
INFO [2024-05-29 19:55:05] $cat.fontface
INFO [2024-05-29 19:55:05] [1] "plain"
INFO [2024-05-29 19:55:05]
INFO [2024-05-29 19:55:05] $cat.fontfamily
INFO [2024-05-29 19:55:05] [1] "serif"
INFO [2024-05-29 19:55:05]
INFO [2024-05-29 19:55:05] $x
INFO [2024-05-29 19:55:05] $x$TF1
INFO [2024-05-29 19:55:05] [1] 4 5 6
INFO [2024-05-29 19:55:05]
INFO [2024-05-29 19:55:05] $x$TF2
INFO [2024-05-29 19:55:05] [1] 1 2 3
INFO [2024-05-29 19:55:05]
INFO [2024-05-29 19:55:05] $x$TF3
INFO [2024-05-29 19:55:05] [1] 2 3 6
INFO [2024-05-29 19:55:05]
INFO [2024-05-29 19:55:05]
INFO [2024-05-29 19:55:05] $disable.logging
INFO [2024-05-29 19:55:05] [1] TRUE
INFO [2024-05-29 19:55:05]
INFO [2024-05-29 19:55:05] $filename
INFO [2024-05-29 19:55:05] NULL
INFO [2024-05-29 19:55:05]
INFO [2024-05-29 19:55:05] $scaled
INFO [2024-05-29 19:55:05] [1] FALSE
INFO [2024-05-29 19:55:05]
INFO [2024-05-29 19:55:05] $euler.d
INFO [2024-05-29 19:55:05] [1] FALSE
INFO [2024-05-29 19:55:05]
INFO [2024-05-29 19:55:05] $cat.cex
INFO [2024-05-29 19:55:05] [1] 1
INFO [2024-05-29 19:55:05]
INFO [2024-05-29 19:55:05] $cat.col
INFO [2024-05-29 19:55:05] [1] "black"
INFO [2024-05-29 19:55:05]
INFO [2024-05-29 19:55:05] $cat.fontface
INFO [2024-05-29 19:55:05] [1] "plain"
INFO [2024-05-29 19:55:05]
INFO [2024-05-29 19:55:05] $cat.fontfamily
INFO [2024-05-29 19:55:05] [1] "serif"
INFO [2024-05-29 19:55:05]
INFO [2024-05-29 19:55:05] $x
INFO [2024-05-29 19:55:05] $x$TF1
INFO [2024-05-29 19:55:05] [1] 3 4 5
INFO [2024-05-29 19:55:05]
INFO [2024-05-29 19:55:05] $x$TF2
INFO [2024-05-29 19:55:05] [1] 1 2 5
INFO [2024-05-29 19:55:05]
INFO [2024-05-29 19:55:05] $x$TF3
INFO [2024-05-29 19:55:05] [1] 1 2 5
INFO [2024-05-29 19:55:05]
INFO [2024-05-29 19:55:05]
INFO [2024-05-29 19:55:05] $disable.logging
INFO [2024-05-29 19:55:05] [1] TRUE
INFO [2024-05-29 19:55:05]
INFO [2024-05-29 19:55:05] $filename
INFO [2024-05-29 19:55:05] NULL
INFO [2024-05-29 19:55:05]
INFO [2024-05-29 19:55:06] $scaled
INFO [2024-05-29 19:55:06] [1] FALSE
INFO [2024-05-29 19:55:06]
INFO [2024-05-29 19:55:06] $euler.d
INFO [2024-05-29 19:55:06] [1] FALSE
INFO [2024-05-29 19:55:06]
INFO [2024-05-29 19:55:06] $cat.cex
INFO [2024-05-29 19:55:06] [1] 1
INFO [2024-05-29 19:55:06]
INFO [2024-05-29 19:55:06] $cat.col
INFO [2024-05-29 19:55:06] [1] "black"
INFO [2024-05-29 19:55:06]
INFO [2024-05-29 19:55:06] $cat.fontface
INFO [2024-05-29 19:55:06] [1] "plain"
INFO [2024-05-29 19:55:06]
INFO [2024-05-29 19:55:06] $cat.fontfamily
INFO [2024-05-29 19:55:06] [1] "serif"
INFO [2024-05-29 19:55:06]
INFO [2024-05-29 19:55:06] $x
INFO [2024-05-29 19:55:06] $x$TF1
INFO [2024-05-29 19:55:06] [1] 3 4 5
INFO [2024-05-29 19:55:06]
INFO [2024-05-29 19:55:06] $x$TF2
INFO [2024-05-29 19:55:06] [1] 1 2 5
INFO [2024-05-29 19:55:06]
INFO [2024-05-29 19:55:06] $x$TF3
INFO [2024-05-29 19:55:06] [1] 1 2 5
INFO [2024-05-29 19:55:06]
INFO [2024-05-29 19:55:06] $x$TF4
INFO [2024-05-29 19:55:06] [1] 1 2 5
INFO [2024-05-29 19:55:06]
INFO [2024-05-29 19:55:06]
INFO [2024-05-29 19:55:06] $disable.logging
INFO [2024-05-29 19:55:06] [1] TRUE
INFO [2024-05-29 19:55:06]
INFO [2024-05-29 19:55:06] $filename
INFO [2024-05-29 19:55:06] NULL
INFO [2024-05-29 19:55:06]
[ 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
204.253 7.478 218.192
ChIPpeakAnno.Rcheck/ChIPpeakAnno-Ex.timings
| name | user | system | elapsed | |
| ChIPpeakAnno-package | 0.000 | 0.000 | 0.001 | |
| ExonPlusUtr.human.GRCh37 | 3.526 | 0.120 | 3.677 | |
| HOT.spots | 0.138 | 0.011 | 0.151 | |
| IDRfilter | 0.002 | 0.000 | 0.001 | |
| Peaks.Ste12.Replicate1 | 0.054 | 0.003 | 0.058 | |
| Peaks.Ste12.Replicate2 | 0.016 | 0.002 | 0.018 | |
| Peaks.Ste12.Replicate3 | 0.014 | 0.003 | 0.017 | |
| TSS.human.GRCh37 | 0.191 | 0.016 | 0.209 | |
| TSS.human.GRCh38 | 0.156 | 0.011 | 0.168 | |
| TSS.human.NCBI36 | 0.112 | 0.010 | 0.123 | |
| TSS.mouse.GRCm38 | 0.108 | 0.011 | 0.121 | |
| TSS.mouse.NCBIM37 | 0.097 | 0.007 | 0.105 | |
| TSS.rat.RGSC3.4 | 0.083 | 0.006 | 0.091 | |
| TSS.rat.Rnor_5.0 | 0.070 | 0.007 | 0.079 | |
| TSS.zebrafish.Zv8 | 0.080 | 0.008 | 0.089 | |
| TSS.zebrafish.Zv9 | 0.089 | 0.010 | 0.100 | |
| addAncestors | 1.406 | 0.084 | 1.504 | |
| addGeneIDs | 2.479 | 0.969 | 3.501 | |
| addMetadata | 1.631 | 0.060 | 1.704 | |
| annoGR | 0.000 | 0.000 | 0.001 | |
| annoPeaks | 3.394 | 0.399 | 4.998 | |
| annotatePeakInBatch | 15.102 | 0.898 | 16.215 | |
| annotatedPeak | 0.052 | 0.003 | 0.056 | |
| assignChromosomeRegion | 0.001 | 0.000 | 0.002 | |
| bdp | 0.001 | 0.001 | 0.000 | |
| binOverFeature | 0.855 | 0.038 | 0.900 | |
| binOverGene | 0.001 | 0.001 | 0.001 | |
| binOverRegions | 0.000 | 0.000 | 0.001 | |
| condenseMatrixByColnames | 0.012 | 0.000 | 0.013 | |
| convert2EntrezID | 0.475 | 0.010 | 0.488 | |
| countPatternInSeqs | 0.171 | 0.007 | 0.179 | |
| cumulativePercentage | 0.000 | 0.001 | 0.000 | |
| downstreams | 0.024 | 0.001 | 0.026 | |
| egOrgMap | 0.000 | 0.000 | 0.001 | |
| enrichedGO | 0.002 | 0.002 | 0.004 | |
| enrichmentPlot | 0.546 | 0.018 | 0.569 | |
| estFragmentLength | 0.001 | 0.001 | 0.000 | |
| estLibSize | 0 | 0 | 0 | |
| featureAlignedDistribution | 0.252 | 0.004 | 0.258 | |
| featureAlignedExtendSignal | 0.002 | 0.000 | 0.002 | |
| featureAlignedHeatmap | 0.342 | 0.005 | 0.352 | |
| featureAlignedSignal | 0.293 | 0.055 | 0.357 | |
| findEnhancers | 30.968 | 1.261 | 32.837 | |
| findMotifsInPromoterSeqs | 18.826 | 0.586 | 19.968 | |
| findOverlappingPeaks | 0.001 | 0.002 | 0.003 | |
| findOverlapsOfPeaks | 2.443 | 0.056 | 2.535 | |
| genomicElementDistribution | 0.003 | 0.001 | 0.003 | |
| genomicElementUpSetR | 0.001 | 0.001 | 0.001 | |
| getAllPeakSequence | 0.685 | 0.035 | 0.734 | |
| getAnnotation | 0.001 | 0.001 | 0.003 | |
| getEnrichedGO | 0.012 | 0.009 | 0.021 | |
| getEnrichedPATH | 0.001 | 0.001 | 0.002 | |
| getGO | 0.000 | 0.001 | 0.001 | |
| getGeneSeq | 0.002 | 0.001 | 0.004 | |
| getUniqueGOidCount | 0.001 | 0.000 | 0.001 | |
| getVennCounts | 0.002 | 0.000 | 0.001 | |
| hyperGtest | 0.001 | 0.001 | 0.002 | |
| makeVennDiagram | 0.004 | 0.001 | 0.005 | |
| mergePlusMinusPeaks | 0.001 | 0.001 | 0.001 | |
| metagenePlot | 2.548 | 0.082 | 2.667 | |
| myPeakList | 0.017 | 0.003 | 0.019 | |
| oligoFrequency | 0.139 | 0.011 | 0.153 | |
| oligoSummary | 0.001 | 0.000 | 0.001 | |
| peakPermTest | 0.002 | 0.000 | 0.002 | |
| peaks1 | 0.009 | 0.002 | 0.012 | |
| peaks2 | 0.010 | 0.003 | 0.013 | |
| peaks3 | 0.011 | 0.002 | 0.013 | |
| peaksNearBDP | 0.001 | 0.000 | 0.002 | |
| pie1 | 0.006 | 0.002 | 0.007 | |
| plotBinOverRegions | 0.001 | 0.001 | 0.001 | |
| preparePool | 0.001 | 0.000 | 0.001 | |
| reCenterPeaks | 0.032 | 0.000 | 0.032 | |
| summarizeOverlapsByBins | 5.803 | 0.610 | 6.169 | |
| summarizePatternInPeaks | 1.843 | 0.259 | 2.151 | |
| tileCount | 0.449 | 0.412 | 0.541 | |
| tileGRanges | 0.045 | 0.023 | 0.071 | |
| toGRanges | 0.107 | 0.017 | 0.126 | |
| translatePattern | 0.000 | 0.000 | 0.001 | |
| wgEncodeTfbsV3 | 0.239 | 0.018 | 0.269 | |
| write2FASTA | 0.020 | 0.003 | 0.024 | |
| xget | 0.147 | 0.018 | 0.175 | |