Multiple platform build/check report for BioC 3.14 - CHECK results for ChIPpeakAnno on tokay2

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This page was generated on 2022-04-13 12:06:19 -0400 (Wed, 13 Apr 2022).

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4137
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*

CHECK results for ChIPpeakAnno on tokay2

To the developers/maintainers of the ChIPpeakAnno package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

ChIPpeakAnno 3.28.1 (landing page)
Jianhong Ou

Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)

git_url: https://git.bioconductor.org/packages/ChIPpeakAnno

git_branch: RELEASE_3_14

git_last_commit: b25b79c

git_last_commit_date: 2022-02-04 15:06:47 -0400 (Fri, 04 Feb 2022)

nebbiolo2

Linux (Ubuntu 20.04.4 LTS) / x86_64

tokay2

Windows Server 2012 R2 Standard / x64

machv2

macOS 10.14.6 Mojave / x86_64

Summary

Package: ChIPpeakAnno

Version: 3.28.1

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChIPpeakAnno.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ChIPpeakAnno_3.28.1.tar.gz

StartedAt: 2022-04-12 17:12:12 -0400 (Tue, 12 Apr 2022)

EndedAt: 2022-04-12 17:31:36 -0400 (Tue, 12 Apr 2022)

EllapsedTime: 1163.4 seconds

RetCode: 0

Status: OK

CheckDir: ChIPpeakAnno.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChIPpeakAnno.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ChIPpeakAnno_3.28.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/ChIPpeakAnno.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ChIPpeakAnno/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ChIPpeakAnno' version '3.28.1'
* 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 whether package 'ChIPpeakAnno' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 19.7Mb
  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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
findEnhancers            31.82   0.35   32.24
findMotifsInPromoterSeqs 14.93   0.92   18.28
annotatePeakInBatch      14.08   0.62   14.70
annoPeaks                 3.62   0.38    6.66
summarizeOverlapsByBins   2.78   0.08   20.24
tileCount                 1.25   0.00   19.62
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
findEnhancers            31.43   0.34   31.77
annotatePeakInBatch      17.10   0.50   17.64
findMotifsInPromoterSeqs 13.64   0.17   13.81
annoPeaks                 3.48   0.24    6.02
summarizeOverlapsByBins   3.17   0.02   23.05
tileCount                 1.39   0.02   20.70
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... 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
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/ChIPpeakAnno.Rcheck/00check.log'
for details.

Installation output

ChIPpeakAnno.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/ChIPpeakAnno_3.28.1.tar.gz && rm -rf ChIPpeakAnno.buildbin-libdir && mkdir ChIPpeakAnno.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ChIPpeakAnno.buildbin-libdir ChIPpeakAnno_3.28.1.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL ChIPpeakAnno_3.28.1.zip && rm ChIPpeakAnno_3.28.1.tar.gz ChIPpeakAnno_3.28.1.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  4 15.7M    4  797k    0     0  1248k      0  0:00:12 --:--:--  0:00:12 1249k
 18 15.7M   18 3025k    0     0  1849k      0  0:00:08  0:00:01  0:00:07 1849k
 38 15.7M   38 6165k    0     0  2342k      0  0:00:06  0:00:02  0:00:04 2342k
 63 15.7M   63 10.0M    0     0  2812k      0  0:00:05  0:00:03  0:00:02 2812k
 94 15.7M   94 14.8M    0     0  3277k      0  0:00:04  0:00:04 --:--:-- 3277k
100 15.7M  100 15.7M    0     0  3357k      0  0:00:04  0:00:04 --:--:-- 3682k

install for i386

* 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
  converting help for package 'ChIPpeakAnno'
    finding HTML links ... done
    ChIPpeakAnno-deprecated                 html  
    ChIPpeakAnno-package                    html  
    EnsDb2GR                                html  
    ExonPlusUtr.human.GRCh37                html  
    HOT.spots                               html  
    IDRfilter                               html  
    Peaks.Ste12.Replicate1                  html  
    Peaks.Ste12.Replicate2                  html  
    Peaks.Ste12.Replicate3                  html  
    TSS.human.GRCh37                        html  
    TSS.human.GRCh38                        html  
    TSS.human.NCBI36                        html  
    TSS.mouse.GRCm38                        html  
    TSS.mouse.NCBIM37                       html  
    TSS.rat.RGSC3.4                         html  
    TSS.rat.Rnor_5.0                        html  
    TSS.zebrafish.Zv8                       html  
    TSS.zebrafish.Zv9                       html  
    TxDb2GR                                 html  
    addAncestors                            html  
    addGeneIDs                              html  
    addMetadata                             html  
    annoGR                                  html  
    annoPeaks                               html  
    annotatePeakInBatch                     html  
    annotatedPeak                           html  
    assignChromosomeRegion                  html  
    bdp                                     html  
    binOverFeature                          html  
    binOverGene                             html  
    binOverRegions                          html  
    bindist                                 html  
    cntOverlaps                             html  
    condenseMatrixByColnames                html  
    convert2EntrezID                        html  
    countPatternInSeqs                      html  
    cumulativePercentage                    html  
    downstreams                             html  
    egOrgMap                                html  
    enrichedGO                              html  
    enrichmentPlot                          html  
    estFragmentLength                       html  
    estLibSize                              html  
    featureAlignedDistribution              html  
    featureAlignedExtendSignal              html  
    featureAlignedHeatmap                   html  
    featureAlignedSignal                    html  
    findEnhancers                           html  
    findMotifsInPromoterSeqs                html  
    findOverlappingPeaks                    html  
    findOverlapsOfPeaks                     html  
    genomicElementDistribution              html  
    genomicElementUpSetR                    html  
    getAllPeakSequence                      html  
    getAnnotation                           html  
    getEnrichedGO                           html  
    getEnrichedPATH                         html  
    getGO                                   html  
    getGeneSeq                              html  
    getUniqueGOidCount                      html  
    getVennCounts                           html  
    hyperGtest                              html  
    makeVennDiagram                         html  
    mergePlusMinusPeaks                     html  
    metagenePlot                            html  
    myPeakList                              html  
    oligoFrequency                          html  
    oligoSummary                            html  
    peakPermTest                            html  
    peaksNearBDP                            html  
    permPool                                html  
    pie1                                    html  
    plotBinOverRegions                      html  
    preparePool                             html  
    reCenterPeaks                           html  
    summarizeOverlapsByBins                 html  
    summarizePatternInPeaks                 html  
    tileCount                               html  
    tileGRanges                             html  
    toGRanges                               html  
    translatePattern                        html  
    wgEncodeTfbsV3                          html  
    write2FASTA                             html  
    xget                                    html  
** 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

install for x64

* installing *source* package 'ChIPpeakAnno' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ChIPpeakAnno' as ChIPpeakAnno_3.28.1.zip
* DONE (ChIPpeakAnno)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'ChIPpeakAnno' successfully unpacked and MD5 sums checked

Tests output

ChIPpeakAnno.Rcheck/tests_i386/runTests.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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, 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 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: 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("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")
[ FAIL 0 | WARN 3 | SKIP 6 | PASS 313 ]

== Skipped tests ===============================================================
* empty test (6)

[ FAIL 0 | WARN 3 | SKIP 6 | PASS 313 ]
> 
> proc.time()
   user  system elapsed 
 197.90    6.23  220.29

ChIPpeakAnno.Rcheck/tests_x64/runTests.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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, 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 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: 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("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")
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
In addition: Warning message:
call dbDisconnect() when finished working with a connection 
[ FAIL 0 | WARN 3 | SKIP 6 | PASS 313 ]

== Skipped tests ===============================================================
* empty test (6)

[ FAIL 0 | WARN 3 | SKIP 6 | PASS 313 ]
> 
> proc.time()
   user  system elapsed 
 200.87    3.62  217.21

Example timings

ChIPpeakAnno.Rcheck/examples_i386/ChIPpeakAnno-Ex.timings

name	user	system	elapsed
ChIPpeakAnno-package	0	0	0
ExonPlusUtr.human.GRCh37	3.63	0.09	3.72
HOT.spots	0.19	0.02	0.21
IDRfilter	0	0	0
Peaks.Ste12.Replicate1	0.06	0.02	0.07
Peaks.Ste12.Replicate2	0.02	0.00	0.02
Peaks.Ste12.Replicate3	0.02	0.00	0.01
TSS.human.GRCh37	0.19	0.03	0.22
TSS.human.GRCh38	0.17	0.04	0.22
TSS.human.NCBI36	0.16	0.00	0.15
TSS.mouse.GRCm38	0.12	0.03	0.16
TSS.mouse.NCBIM37	0.11	0.04	0.14
TSS.rat.RGSC3.4	0.11	0.00	0.11
TSS.rat.Rnor_5.0	0.08	0.03	0.11
TSS.zebrafish.Zv8	0.11	0.00	0.11
TSS.zebrafish.Zv9	0.11	0.01	0.12
addAncestors	1.17	0.11	1.29
addGeneIDs	2.22	1.72	3.95
addMetadata	1.74	0.06	1.80
annoGR	0	0	0
annoPeaks	3.62	0.38	6.66
annotatePeakInBatch	14.08	0.62	14.70
annotatedPeak	0.08	0.00	0.07
assignChromosomeRegion	0	0	0
bdp	0	0	0
binOverFeature	1.43	0.02	1.47
binOverGene	0	0	0
binOverRegions	0	0	0
condenseMatrixByColnames	0.02	0.00	0.02
convert2EntrezID	0.34	0.00	0.34
countPatternInSeqs	0.17	0.00	0.17
cumulativePercentage	0	0	0
downstreams	0.05	0.00	0.05
egOrgMap	0	0	0
enrichedGO	0.00	0.01	0.02
enrichmentPlot	0.5	0.0	0.5
estFragmentLength	0	0	0
estLibSize	0	0	0
featureAlignedDistribution	0.28	0.00	0.28
featureAlignedExtendSignal	0	0	0
featureAlignedHeatmap	0.47	0.00	0.47
featureAlignedSignal	0.27	0.00	0.26
findEnhancers	31.82	0.35	32.24
findMotifsInPromoterSeqs	14.93	0.92	18.28
findOverlappingPeaks	0	0	0
findOverlapsOfPeaks	3.47	0.00	3.47
genomicElementDistribution	0	0	0
genomicElementUpSetR	0	0	0
getAllPeakSequence	0.76	0.00	0.76
getAnnotation	0	0	0
getEnrichedGO	0.02	0.00	0.02
getEnrichedPATH	0	0	0
getGO	0	0	0
getGeneSeq	0	0	0
getUniqueGOidCount	0	0	0
getVennCounts	0.01	0.00	0.01
hyperGtest	0	0	0
makeVennDiagram	0	0	0
mergePlusMinusPeaks	0	0	0
metagenePlot	3.27	0.30	3.61
myPeakList	0.01	0.01	0.03
oligoFrequency	0.18	0.02	0.19
oligoSummary	0	0	0
peakPermTest	0	0	0
peaksNearBDP	0	0	0
pie1	0.01	0.00	0.02
plotBinOverRegions	0	0	0
preparePool	0	0	0
reCenterPeaks	0.05	0.00	0.04
summarizeOverlapsByBins	2.78	0.08	20.24
summarizePatternInPeaks	0.78	0.00	0.78
tileCount	1.25	0.00	19.62
tileGRanges	0.11	0.00	0.11
toGRanges	0.19	0.00	0.19
translatePattern	0	0	0
wgEncodeTfbsV3	0.39	0.00	0.39
write2FASTA	0.03	0.00	0.03
xget	0.08	0.02	0.09

ChIPpeakAnno.Rcheck/examples_x64/ChIPpeakAnno-Ex.timings

name	user	system	elapsed
ChIPpeakAnno-package	0	0	0
ExonPlusUtr.human.GRCh37	4.86	0.14	5.00
HOT.spots	0.19	0.03	0.22
IDRfilter	0	0	0
Peaks.Ste12.Replicate1	0.11	0.00	0.11
Peaks.Ste12.Replicate2	0.04	0.00	0.04
Peaks.Ste12.Replicate3	0.04	0.00	0.03
TSS.human.GRCh37	0.28	0.03	0.32
TSS.human.GRCh38	0.18	0.03	0.21
TSS.human.NCBI36	0.15	0.02	0.16
TSS.mouse.GRCm38	0.14	0.03	0.17
TSS.mouse.NCBIM37	0.14	0.00	0.14
TSS.rat.RGSC3.4	0.11	0.01	0.13
TSS.rat.Rnor_5.0	0.11	0.00	0.11
TSS.zebrafish.Zv8	0.10	0.00	0.11
TSS.zebrafish.Zv9	0.13	0.00	0.12
addAncestors	1.80	0.13	1.92
addGeneIDs	3.15	1.09	4.25
addMetadata	2.19	0.17	2.36
annoGR	0	0	0
annoPeaks	3.48	0.24	6.02
annotatePeakInBatch	17.10	0.50	17.64
annotatedPeak	0.07	0.00	0.06
assignChromosomeRegion	0	0	0
bdp	0	0	0
binOverFeature	1.09	0.06	1.15
binOverGene	0	0	0
binOverRegions	0	0	0
condenseMatrixByColnames	0.02	0.00	0.02
convert2EntrezID	0.34	0.00	0.34
countPatternInSeqs	0.17	0.00	0.18
cumulativePercentage	0	0	0
downstreams	0.05	0.00	0.04
egOrgMap	0	0	0
enrichedGO	0	0	0
enrichmentPlot	0.44	0.02	0.46
estFragmentLength	0	0	0
estLibSize	0	0	0
featureAlignedDistribution	0.31	0.00	0.31
featureAlignedExtendSignal	0	0	0
featureAlignedHeatmap	0.56	0.00	0.56
featureAlignedSignal	0.34	0.00	0.34
findEnhancers	31.43	0.34	31.77
findMotifsInPromoterSeqs	13.64	0.17	13.81
findOverlappingPeaks	0	0	0
findOverlapsOfPeaks	3.54	0.00	3.55
genomicElementDistribution	0	0	0
genomicElementUpSetR	0	0	0
getAllPeakSequence	0.8	0.0	0.8
getAnnotation	0	0	0
getEnrichedGO	0.02	0.00	0.01
getEnrichedPATH	0	0	0
getGO	0	0	0
getGeneSeq	0.01	0.00	0.02
getUniqueGOidCount	0	0	0
getVennCounts	0	0	0
hyperGtest	0	0	0
makeVennDiagram	0	0	0
mergePlusMinusPeaks	0	0	0
metagenePlot	2.64	0.05	2.68
myPeakList	0.02	0.00	0.02
oligoFrequency	0.15	0.02	0.20
oligoSummary	0	0	0
peakPermTest	0	0	0
peaksNearBDP	0	0	0
pie1	0	0	0
plotBinOverRegions	0	0	0
preparePool	0	0	0
reCenterPeaks	0.05	0.00	0.05
summarizeOverlapsByBins	3.17	0.02	23.05
summarizePatternInPeaks	0.81	0.01	0.83
tileCount	1.39	0.02	20.70
tileGRanges	0.08	0.00	0.08
toGRanges	0.17	0.00	0.17
translatePattern	0	0	0
wgEncodeTfbsV3	0.25	0.01	0.27
write2FASTA	0.01	0.00	0.02
xget	0.14	0.00	0.14