Jianhong Ou
| Snapshot Date: 2024-06-26 14:00 -0400 (Wed, 26 Jun 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 2024-06-28 17:41 -0400 (Fri, 28 Jun 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" | 4760 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4494 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4508 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4466 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4362 |
| 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 | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | TIMEOUT | skipped | skipped | |||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
|
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: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ChIPpeakAnno.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings ChIPpeakAnno_3.38.0.tar.gz |
| StartedAt: 2024-06-27 00:01:12 -0400 (Thu, 27 Jun 2024) |
| EndedAt: 2024-06-27 00:15:44 -0400 (Thu, 27 Jun 2024) |
| EllapsedTime: 872.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ChIPpeakAnno.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ChIPpeakAnno.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings ChIPpeakAnno_3.38.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/ChIPpeakAnno.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 whether package 'ChIPpeakAnno' can be installed ... OK
* checking installed package size ... NOTE
installed size is 21.1Mb
sub-directories of 1Mb or more:
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 30.44 1.48 36.71
findMotifsInPromoterSeqs 18.34 0.88 30.95
annotatePeakInBatch 16.71 1.38 19.14
addGeneIDs 3.32 1.66 5.02
summarizeOverlapsByBins 4.39 0.06 26.74
annoPeaks 3.37 0.58 5.32
addAncestors 1.53 0.23 7.51
tileCount 1.54 0.04 23.28
* 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
'F:/biocbuild/bbs-3.19-bioc/meat/ChIPpeakAnno.Rcheck/00check.log'
for details.
ChIPpeakAnno.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL ChIPpeakAnno ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.19-bioc/R/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 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
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 [2024-06-27 00:15:09] $cat.cex
INFO [2024-06-27 00:15:09] [1] 1
INFO [2024-06-27 00:15:09]
INFO [2024-06-27 00:15:09] $cat.col
INFO [2024-06-27 00:15:09] [1] "black"
INFO [2024-06-27 00:15:09]
INFO [2024-06-27 00:15:09] $cat.fontface
INFO [2024-06-27 00:15:09] [1] "plain"
INFO [2024-06-27 00:15:09]
INFO [2024-06-27 00:15:09] $cat.fontfamily
INFO [2024-06-27 00:15:09] [1] "serif"
INFO [2024-06-27 00:15:09]
INFO [2024-06-27 00:15:09] $x
INFO [2024-06-27 00:15:09] $x$TF1
INFO [2024-06-27 00:15:09] [1] 3 4 5
INFO [2024-06-27 00:15:09]
INFO [2024-06-27 00:15:09] $x$TF2
INFO [2024-06-27 00:15:09] [1] 1 2 3 4 5
INFO [2024-06-27 00:15:09]
INFO [2024-06-27 00:15:09]
INFO [2024-06-27 00:15:09] $disable.logging
INFO [2024-06-27 00:15:09] [1] TRUE
INFO [2024-06-27 00:15:09]
INFO [2024-06-27 00:15:09] $filename
INFO [2024-06-27 00:15:09] NULL
INFO [2024-06-27 00:15:09]
INFO [2024-06-27 00:15:09] $cat.cex
INFO [2024-06-27 00:15:09] [1] 1
INFO [2024-06-27 00:15:09]
INFO [2024-06-27 00:15:09] $cat.col
INFO [2024-06-27 00:15:09] [1] "black"
INFO [2024-06-27 00:15:09]
INFO [2024-06-27 00:15:09] $cat.fontface
INFO [2024-06-27 00:15:09] [1] "plain"
INFO [2024-06-27 00:15:09]
INFO [2024-06-27 00:15:09] $cat.fontfamily
INFO [2024-06-27 00:15:09] [1] "serif"
INFO [2024-06-27 00:15:09]
INFO [2024-06-27 00:15:09] $x
INFO [2024-06-27 00:15:09] $x$TF1
INFO [2024-06-27 00:15:09] [1] 3 4 5
INFO [2024-06-27 00:15:09]
INFO [2024-06-27 00:15:09] $x$TF2
INFO [2024-06-27 00:15:09] [1] 1 2 4 5
INFO [2024-06-27 00:15:09]
INFO [2024-06-27 00:15:09] $x$TF3
INFO [2024-06-27 00:15:09] [1] 3 4 5
INFO [2024-06-27 00:15:09]
INFO [2024-06-27 00:15:09] $x$TF4
INFO [2024-06-27 00:15:09] [1] 1 2 4 5
INFO [2024-06-27 00:15:09]
INFO [2024-06-27 00:15:09]
INFO [2024-06-27 00:15:09] $disable.logging
INFO [2024-06-27 00:15:09] [1] TRUE
INFO [2024-06-27 00:15:09]
INFO [2024-06-27 00:15:09] $filename
INFO [2024-06-27 00:15:09] NULL
INFO [2024-06-27 00:15:09]
INFO [2024-06-27 00:15:10] $scaled
INFO [2024-06-27 00:15:10] [1] FALSE
INFO [2024-06-27 00:15:10]
INFO [2024-06-27 00:15:10] $euler.d
INFO [2024-06-27 00:15:10] [1] FALSE
INFO [2024-06-27 00:15:10]
INFO [2024-06-27 00:15:10] $cat.cex
INFO [2024-06-27 00:15:10] [1] 1
INFO [2024-06-27 00:15:10]
INFO [2024-06-27 00:15:10] $cat.col
INFO [2024-06-27 00:15:10] [1] "black"
INFO [2024-06-27 00:15:10]
INFO [2024-06-27 00:15:10] $cat.fontface
INFO [2024-06-27 00:15:10] [1] "plain"
INFO [2024-06-27 00:15:10]
INFO [2024-06-27 00:15:10] $cat.fontfamily
INFO [2024-06-27 00:15:10] [1] "serif"
INFO [2024-06-27 00:15:10]
INFO [2024-06-27 00:15:10] $x
INFO [2024-06-27 00:15:10] $x$TF1
INFO [2024-06-27 00:15:10] [1] 1 2 3
INFO [2024-06-27 00:15:10]
INFO [2024-06-27 00:15:10] $x$TF2
INFO [2024-06-27 00:15:10] [1] 1 2 3
INFO [2024-06-27 00:15:10]
INFO [2024-06-27 00:15:10]
INFO [2024-06-27 00:15:10] $disable.logging
INFO [2024-06-27 00:15:10] [1] TRUE
INFO [2024-06-27 00:15:10]
INFO [2024-06-27 00:15:10] $filename
INFO [2024-06-27 00:15:10] NULL
INFO [2024-06-27 00:15:10]
INFO [2024-06-27 00:15:10] $scaled
INFO [2024-06-27 00:15:10] [1] FALSE
INFO [2024-06-27 00:15:10]
INFO [2024-06-27 00:15:10] $euler.d
INFO [2024-06-27 00:15:10] [1] FALSE
INFO [2024-06-27 00:15:10]
INFO [2024-06-27 00:15:10] $cat.cex
INFO [2024-06-27 00:15:10] [1] 1
INFO [2024-06-27 00:15:10]
INFO [2024-06-27 00:15:10] $cat.col
INFO [2024-06-27 00:15:10] [1] "black"
INFO [2024-06-27 00:15:10]
INFO [2024-06-27 00:15:10] $cat.fontface
INFO [2024-06-27 00:15:10] [1] "plain"
INFO [2024-06-27 00:15:10]
INFO [2024-06-27 00:15:10] $cat.fontfamily
INFO [2024-06-27 00:15:10] [1] "serif"
INFO [2024-06-27 00:15:10]
INFO [2024-06-27 00:15:10] $x
INFO [2024-06-27 00:15:10] $x$TF1
INFO [2024-06-27 00:15:10] [1] 4 5 6
INFO [2024-06-27 00:15:10]
INFO [2024-06-27 00:15:10] $x$TF2
INFO [2024-06-27 00:15:10] [1] 1 2 3
INFO [2024-06-27 00:15:10]
INFO [2024-06-27 00:15:10]
INFO [2024-06-27 00:15:10] $disable.logging
INFO [2024-06-27 00:15:10] [1] TRUE
INFO [2024-06-27 00:15:10]
INFO [2024-06-27 00:15:10] $filename
INFO [2024-06-27 00:15:10] NULL
INFO [2024-06-27 00:15:10]
INFO [2024-06-27 00:15:11] $scaled
INFO [2024-06-27 00:15:11] [1] FALSE
INFO [2024-06-27 00:15:11]
INFO [2024-06-27 00:15:11] $euler.d
INFO [2024-06-27 00:15:11] [1] FALSE
INFO [2024-06-27 00:15:11]
INFO [2024-06-27 00:15:11] $cat.cex
INFO [2024-06-27 00:15:11] [1] 1
INFO [2024-06-27 00:15:11]
INFO [2024-06-27 00:15:11] $cat.col
INFO [2024-06-27 00:15:11] [1] "black"
INFO [2024-06-27 00:15:11]
INFO [2024-06-27 00:15:11] $cat.fontface
INFO [2024-06-27 00:15:11] [1] "plain"
INFO [2024-06-27 00:15:11]
INFO [2024-06-27 00:15:11] $cat.fontfamily
INFO [2024-06-27 00:15:11] [1] "serif"
INFO [2024-06-27 00:15:11]
INFO [2024-06-27 00:15:11] $x
INFO [2024-06-27 00:15:11] $x$TF1
INFO [2024-06-27 00:15:11] [1] 4 5 6
INFO [2024-06-27 00:15:11]
INFO [2024-06-27 00:15:11] $x$TF2
INFO [2024-06-27 00:15:11] [1] 1 2 3
INFO [2024-06-27 00:15:11]
INFO [2024-06-27 00:15:11]
INFO [2024-06-27 00:15:11] $disable.logging
INFO [2024-06-27 00:15:11] [1] TRUE
INFO [2024-06-27 00:15:11]
INFO [2024-06-27 00:15:11] $filename
INFO [2024-06-27 00:15:11] NULL
INFO [2024-06-27 00:15:11]
INFO [2024-06-27 00:15:11] $scaled
INFO [2024-06-27 00:15:11] [1] FALSE
INFO [2024-06-27 00:15:11]
INFO [2024-06-27 00:15:11] $euler.d
INFO [2024-06-27 00:15:11] [1] FALSE
INFO [2024-06-27 00:15:11]
INFO [2024-06-27 00:15:11] $cat.cex
INFO [2024-06-27 00:15:11] [1] 1
INFO [2024-06-27 00:15:11]
INFO [2024-06-27 00:15:11] $cat.col
INFO [2024-06-27 00:15:11] [1] "black"
INFO [2024-06-27 00:15:11]
INFO [2024-06-27 00:15:11] $cat.fontface
INFO [2024-06-27 00:15:11] [1] "plain"
INFO [2024-06-27 00:15:11]
INFO [2024-06-27 00:15:11] $cat.fontfamily
INFO [2024-06-27 00:15:11] [1] "serif"
INFO [2024-06-27 00:15:11]
INFO [2024-06-27 00:15:11] $x
INFO [2024-06-27 00:15:11] $x$TF1
INFO [2024-06-27 00:15:11] [1] 4 5 6
INFO [2024-06-27 00:15:11]
INFO [2024-06-27 00:15:11] $x$TF2
INFO [2024-06-27 00:15:11] [1] 1 2 3
INFO [2024-06-27 00:15:11]
INFO [2024-06-27 00:15:11] $x$TF3
INFO [2024-06-27 00:15:11] [1] 2 3 6
INFO [2024-06-27 00:15:11]
INFO [2024-06-27 00:15:11]
INFO [2024-06-27 00:15:11] $disable.logging
INFO [2024-06-27 00:15:11] [1] TRUE
INFO [2024-06-27 00:15:11]
INFO [2024-06-27 00:15:11] $filename
INFO [2024-06-27 00:15:11] NULL
INFO [2024-06-27 00:15:11]
INFO [2024-06-27 00:15:12] $scaled
INFO [2024-06-27 00:15:12] [1] FALSE
INFO [2024-06-27 00:15:12]
INFO [2024-06-27 00:15:12] $euler.d
INFO [2024-06-27 00:15:12] [1] FALSE
INFO [2024-06-27 00:15:12]
INFO [2024-06-27 00:15:12] $cat.cex
INFO [2024-06-27 00:15:12] [1] 1
INFO [2024-06-27 00:15:12]
INFO [2024-06-27 00:15:12] $cat.col
INFO [2024-06-27 00:15:12] [1] "black"
INFO [2024-06-27 00:15:12]
INFO [2024-06-27 00:15:12] $cat.fontface
INFO [2024-06-27 00:15:12] [1] "plain"
INFO [2024-06-27 00:15:12]
INFO [2024-06-27 00:15:12] $cat.fontfamily
INFO [2024-06-27 00:15:12] [1] "serif"
INFO [2024-06-27 00:15:12]
INFO [2024-06-27 00:15:12] $x
INFO [2024-06-27 00:15:12] $x$TF1
INFO [2024-06-27 00:15:12] [1] 3 4 5
INFO [2024-06-27 00:15:12]
INFO [2024-06-27 00:15:12] $x$TF2
INFO [2024-06-27 00:15:12] [1] 1 2 5
INFO [2024-06-27 00:15:12]
INFO [2024-06-27 00:15:12] $x$TF3
INFO [2024-06-27 00:15:12] [1] 1 2 5
INFO [2024-06-27 00:15:12]
INFO [2024-06-27 00:15:12]
INFO [2024-06-27 00:15:12] $disable.logging
INFO [2024-06-27 00:15:12] [1] TRUE
INFO [2024-06-27 00:15:12]
INFO [2024-06-27 00:15:12] $filename
INFO [2024-06-27 00:15:12] NULL
INFO [2024-06-27 00:15:12]
INFO [2024-06-27 00:15:12] $scaled
INFO [2024-06-27 00:15:12] [1] FALSE
INFO [2024-06-27 00:15:12]
INFO [2024-06-27 00:15:12] $euler.d
INFO [2024-06-27 00:15:12] [1] FALSE
INFO [2024-06-27 00:15:12]
INFO [2024-06-27 00:15:12] $cat.cex
INFO [2024-06-27 00:15:12] [1] 1
INFO [2024-06-27 00:15:12]
INFO [2024-06-27 00:15:12] $cat.col
INFO [2024-06-27 00:15:12] [1] "black"
INFO [2024-06-27 00:15:12]
INFO [2024-06-27 00:15:12] $cat.fontface
INFO [2024-06-27 00:15:12] [1] "plain"
INFO [2024-06-27 00:15:12]
INFO [2024-06-27 00:15:12] $cat.fontfamily
INFO [2024-06-27 00:15:12] [1] "serif"
INFO [2024-06-27 00:15:12]
INFO [2024-06-27 00:15:12] $x
INFO [2024-06-27 00:15:12] $x$TF1
INFO [2024-06-27 00:15:12] [1] 3 4 5
INFO [2024-06-27 00:15:12]
INFO [2024-06-27 00:15:12] $x$TF2
INFO [2024-06-27 00:15:12] [1] 1 2 5
INFO [2024-06-27 00:15:12]
INFO [2024-06-27 00:15:12] $x$TF3
INFO [2024-06-27 00:15:12] [1] 1 2 5
INFO [2024-06-27 00:15:12]
INFO [2024-06-27 00:15:12] $x$TF4
INFO [2024-06-27 00:15:12] [1] 1 2 5
INFO [2024-06-27 00:15:12]
INFO [2024-06-27 00:15:12]
INFO [2024-06-27 00:15:12] $disable.logging
INFO [2024-06-27 00:15:12] [1] TRUE
INFO [2024-06-27 00:15:12]
INFO [2024-06-27 00:15:12] $filename
INFO [2024-06-27 00:15:12] NULL
INFO [2024-06-27 00:15:12]
[ 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
228.12 11.03 274.73
ChIPpeakAnno.Rcheck/ChIPpeakAnno-Ex.timings
| name | user | system | elapsed | |
| ChIPpeakAnno-package | 0 | 0 | 0 | |
| ExonPlusUtr.human.GRCh37 | 3.98 | 0.13 | 4.11 | |
| HOT.spots | 0.11 | 0.03 | 0.14 | |
| IDRfilter | 0 | 0 | 0 | |
| Peaks.Ste12.Replicate1 | 0.05 | 0.00 | 0.05 | |
| Peaks.Ste12.Replicate2 | 0.00 | 0.03 | 0.03 | |
| Peaks.Ste12.Replicate3 | 0.01 | 0.00 | 0.02 | |
| TSS.human.GRCh37 | 0.14 | 0.03 | 0.17 | |
| TSS.human.GRCh38 | 0.14 | 0.02 | 0.15 | |
| TSS.human.NCBI36 | 0.11 | 0.03 | 0.15 | |
| TSS.mouse.GRCm38 | 0.12 | 0.00 | 0.13 | |
| TSS.mouse.NCBIM37 | 0.13 | 0.00 | 0.12 | |
| TSS.rat.RGSC3.4 | 0.06 | 0.03 | 0.09 | |
| TSS.rat.Rnor_5.0 | 0.05 | 0.05 | 0.10 | |
| TSS.zebrafish.Zv8 | 0.09 | 0.00 | 0.09 | |
| TSS.zebrafish.Zv9 | 0.13 | 0.00 | 0.13 | |
| addAncestors | 1.53 | 0.23 | 7.51 | |
| addGeneIDs | 3.32 | 1.66 | 5.02 | |
| addMetadata | 1.88 | 0.04 | 1.93 | |
| annoGR | 0 | 0 | 0 | |
| annoPeaks | 3.37 | 0.58 | 5.32 | |
| annotatePeakInBatch | 16.71 | 1.38 | 19.14 | |
| annotatedPeak | 0.06 | 0.01 | 0.07 | |
| assignChromosomeRegion | 0 | 0 | 0 | |
| bdp | 0 | 0 | 0 | |
| binOverFeature | 0.85 | 0.14 | 1.07 | |
| binOverGene | 0 | 0 | 0 | |
| binOverRegions | 0 | 0 | 0 | |
| condenseMatrixByColnames | 0 | 0 | 0 | |
| convert2EntrezID | 0.61 | 0.00 | 0.61 | |
| countPatternInSeqs | 0.18 | 0.05 | 0.23 | |
| cumulativePercentage | 0 | 0 | 0 | |
| downstreams | 0.04 | 0.00 | 0.03 | |
| egOrgMap | 0 | 0 | 0 | |
| enrichedGO | 0 | 0 | 0 | |
| enrichmentPlot | 0.67 | 0.03 | 0.70 | |
| estFragmentLength | 0 | 0 | 0 | |
| estLibSize | 0 | 0 | 0 | |
| featureAlignedDistribution | 0.20 | 0.01 | 0.22 | |
| featureAlignedExtendSignal | 0 | 0 | 0 | |
| featureAlignedHeatmap | 0.50 | 0.02 | 0.51 | |
| featureAlignedSignal | 0.26 | 0.05 | 0.31 | |
| findEnhancers | 30.44 | 1.48 | 36.71 | |
| findMotifsInPromoterSeqs | 18.34 | 0.88 | 30.95 | |
| findOverlappingPeaks | 0 | 0 | 0 | |
| findOverlapsOfPeaks | 2.07 | 0.03 | 2.15 | |
| genomicElementDistribution | 0 | 0 | 0 | |
| genomicElementUpSetR | 0 | 0 | 0 | |
| getAllPeakSequence | 0.76 | 0.10 | 0.99 | |
| getAnnotation | 0 | 0 | 0 | |
| getEnrichedGO | 0.00 | 0.00 | 0.05 | |
| getEnrichedPATH | 0 | 0 | 0 | |
| getGO | 0 | 0 | 0 | |
| getGeneSeq | 0 | 0 | 0 | |
| getUniqueGOidCount | 0 | 0 | 0 | |
| getVennCounts | 0 | 0 | 0 | |
| hyperGtest | 0 | 0 | 0 | |
| makeVennDiagram | 0.01 | 0.00 | 0.01 | |
| mergePlusMinusPeaks | 0 | 0 | 0 | |
| metagenePlot | 2.61 | 0.14 | 2.96 | |
| myPeakList | 0.01 | 0.03 | 0.03 | |
| oligoFrequency | 0.14 | 0.01 | 0.16 | |
| oligoSummary | 0 | 0 | 0 | |
| peakPermTest | 0 | 0 | 0 | |
| peaks1 | 0.00 | 0.02 | 0.02 | |
| peaks2 | 0 | 0 | 0 | |
| peaks3 | 0 | 0 | 0 | |
| peaksNearBDP | 0.00 | 0.02 | 0.01 | |
| pie1 | 0 | 0 | 0 | |
| plotBinOverRegions | 0 | 0 | 0 | |
| preparePool | 0 | 0 | 0 | |
| reCenterPeaks | 0.04 | 0.00 | 0.03 | |
| summarizeOverlapsByBins | 4.39 | 0.06 | 26.74 | |
| summarizePatternInPeaks | 1.70 | 0.11 | 1.83 | |
| tileCount | 1.54 | 0.04 | 23.28 | |
| tileGRanges | 0.06 | 0.00 | 0.07 | |
| toGRanges | 0.11 | 0.00 | 0.12 | |
| translatePattern | 0 | 0 | 0 | |
| wgEncodeTfbsV3 | 0.22 | 0.04 | 0.25 | |
| write2FASTA | 0.03 | 0.00 | 0.03 | |
| xget | 0.14 | 0.01 | 0.16 | |