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CHECK report for ChIPpeakAnno on tokay1

This page was generated on 2020-08-10 12:12:20 -0400 (Mon, 10 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE ChIPpeakAnno PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 274/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPpeakAnno 3.23.4
Lihua Julie Zhu
Snapshot Date: 2020-08-09 14:51:29 -0400 (Sun, 09 Aug 2020)
URL: https://git.bioconductor.org/packages/ChIPpeakAnno
Branch: master
Last Commit: 538e556
Last Changed Date: 2020-08-04 12:43:36 -0400 (Tue, 04 Aug 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ChIPpeakAnno
Version: 3.23.4
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChIPpeakAnno.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings ChIPpeakAnno_3.23.4.tar.gz
StartedAt: 2020-08-10 00:08:30 -0400 (Mon, 10 Aug 2020)
EndedAt: 2020-08-10 00:23:33 -0400 (Mon, 10 Aug 2020)
EllapsedTime: 902.4 seconds
RetCode: 0
Status:  OK  
CheckDir: ChIPpeakAnno.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChIPpeakAnno.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings ChIPpeakAnno_3.23.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/ChIPpeakAnno.Rcheck'
* using R version 4.0.2 (2020-06-22)
* 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 '3.23.4'
* 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 27.3Mb
  sub-directories of 1Mb or more:
    data     20.5Mb
    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 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            37.14   0.40   37.55
findMotifsInPromoterSeqs 17.15   0.14   17.30
annoPeaks                 3.48   0.62    5.25
summarizeOverlapsByBins   2.88   0.05   21.33
tileCount                 1.17   0.00   15.57
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
findEnhancers            37.21   0.40   37.59
findMotifsInPromoterSeqs 13.61   0.15   13.90
summarizeOverlapsByBins   3.25   0.00   20.06
tileCount                 1.21   0.00   19.78
* 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-3.12-bioc/meat/ChIPpeakAnno.Rcheck/00check.log'
for details.



Installation output

ChIPpeakAnno.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/ChIPpeakAnno_3.23.4.tar.gz && rm -rf ChIPpeakAnno.buildbin-libdir && mkdir ChIPpeakAnno.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ChIPpeakAnno.buildbin-libdir ChIPpeakAnno_3.23.4.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL ChIPpeakAnno_3.23.4.zip && rm ChIPpeakAnno_3.23.4.tar.gz ChIPpeakAnno_3.23.4.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
100 15.6M  100 15.6M    0     0  75.3M      0 --:--:-- --:--:-- --:--:-- 76.9M

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  
    egOrgMap                                html  
    enrichedGO                              html  
    estFragmentLength                       html  
    estLibSize                              html  
    featureAlignedDistribution              html  
    featureAlignedExtendSignal              html  
    featureAlignedHeatmap                   html  
    featureAlignedSignal                    html  
    findEnhancers                           html  
    findMotifsInPromoterSeqs                html  
    findOverlappingPeaks                    html  
    findOverlapsOfPeaks                     html  
    getAllPeakSequence                      html  
    getAnnotation                           html  
    getEnrichedGO                           html  
    getEnrichedPATH                         html  
    getGO                                   html  
    getGeneSeq                              html  
    getUniqueGOidCount                      html  
    getVennCounts                           html  
    hyperGtest                              html  
    makeVennDiagram                         html  
    mergePlusMinusPeaks                     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_3.23.4.zip
* DONE (ChIPpeakAnno)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'ChIPpeakAnno' successfully unpacked and MD5 sums checked

Tests output

ChIPpeakAnno.Rcheck/tests_i386/runTests.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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 object is masked from 'package:base':

    expand.grid


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")
== testthat results  ===========================================================
[ OK: 186 | SKIPPED: 5 | WARNINGS: 1 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 100.06    4.71  112.25 

ChIPpeakAnno.Rcheck/tests_x64/runTests.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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 object is masked from 'package:base':

    expand.grid


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")
== testthat results  ===========================================================
[ OK: 186 | SKIPPED: 5 | WARNINGS: 1 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  90.04    2.48   93.76 

Example timings

ChIPpeakAnno.Rcheck/examples_i386/ChIPpeakAnno-Ex.timings

nameusersystemelapsed
ChIPpeakAnno-package000
ExonPlusUtr.human.GRCh372.890.313.20
HOT.spots0.080.020.09
IDRfilter000
Peaks.Ste12.Replicate10.040.030.08
Peaks.Ste12.Replicate20.020.020.03
Peaks.Ste12.Replicate30.020.000.01
TSS.human.GRCh370.150.010.17
TSS.human.GRCh380.110.020.13
TSS.human.NCBI360.090.030.12
TSS.mouse.GRCm380.110.020.13
TSS.mouse.NCBIM370.080.010.09
TSS.rat.RGSC3.40.060.020.08
TSS.rat.Rnor_5.00.050.010.06
TSS.zebrafish.Zv80.050.020.07
TSS.zebrafish.Zv90.060.050.11
addAncestors1.410.061.46
addGeneIDs2.081.783.86
addMetadata1.530.111.64
annoGR000
annoPeaks3.480.625.25
annotatePeakInBatch4.220.254.46
annotatedPeak0.050.000.05
assignChromosomeRegion000
bdp000
binOverFeature0.730.020.75
binOverGene000
binOverRegions000
condenseMatrixByColnames0.010.000.01
convert2EntrezID0.490.000.49
countPatternInSeqs0.170.000.17
cumulativePercentage000
egOrgMap000
enrichedGO000
estFragmentLength000
estLibSize000
featureAlignedDistribution0.230.000.23
featureAlignedExtendSignal000
featureAlignedHeatmap0.520.000.52
featureAlignedSignal0.440.020.45
findEnhancers37.14 0.4037.55
findMotifsInPromoterSeqs17.15 0.1417.30
findOverlappingPeaks000
findOverlapsOfPeaks0.980.000.99
getAllPeakSequence0.660.000.65
getAnnotation000
getEnrichedGO0.020.000.02
getEnrichedPATH000
getGO000
getGeneSeq000
getUniqueGOidCount000
getVennCounts000
hyperGtest0.010.000.01
makeVennDiagram000
mergePlusMinusPeaks000
myPeakList0.020.000.02
oligoFrequency0.220.000.28
oligoSummary000
peakPermTest000
peaksNearBDP000
pie10.020.000.01
plotBinOverRegions000
preparePool000
reCenterPeaks0.20.00.2
summarizeOverlapsByBins 2.88 0.0521.33
summarizePatternInPeaks0.700.000.71
tileCount 1.17 0.0015.57
tileGRanges0.050.000.05
toGRanges0.150.000.16
translatePattern000
wgEncodeTfbsV30.070.000.06
write2FASTA0.010.000.02
xget0.100.010.10

ChIPpeakAnno.Rcheck/examples_x64/ChIPpeakAnno-Ex.timings

nameusersystemelapsed
ChIPpeakAnno-package000
ExonPlusUtr.human.GRCh372.930.093.02
HOT.spots0.030.020.05
IDRfilter000
Peaks.Ste12.Replicate10.160.030.19
Peaks.Ste12.Replicate20.020.000.01
Peaks.Ste12.Replicate30.010.000.02
TSS.human.GRCh370.060.020.08
TSS.human.GRCh380.080.010.09
TSS.human.NCBI360.050.020.06
TSS.mouse.GRCm380.060.010.08
TSS.mouse.NCBIM370.050.000.05
TSS.rat.RGSC3.40.060.000.06
TSS.rat.Rnor_5.00.030.000.03
TSS.zebrafish.Zv80.060.000.07
TSS.zebrafish.Zv90.240.020.25
addAncestors1.390.041.43
addGeneIDs2.440.823.25
addMetadata2.150.012.17
annoGR000
annoPeaks3.460.304.57
annotatePeakInBatch3.580.083.66
annotatedPeak0.060.000.06
assignChromosomeRegion0.020.000.02
bdp000
binOverFeature0.980.000.98
binOverGene0.000.010.02
binOverRegions000
condenseMatrixByColnames0.020.000.01
convert2EntrezID0.390.000.39
countPatternInSeqs0.150.000.16
cumulativePercentage000
egOrgMap000
enrichedGO0.000.020.02
estFragmentLength000
estLibSize000
featureAlignedDistribution0.470.000.46
featureAlignedExtendSignal000
featureAlignedHeatmap0.530.000.54
featureAlignedSignal0.330.010.34
findEnhancers37.21 0.4037.59
findMotifsInPromoterSeqs13.61 0.1513.90
findOverlappingPeaks000
findOverlapsOfPeaks0.680.000.92
getAllPeakSequence0.770.050.81
getAnnotation000
getEnrichedGO0.010.000.02
getEnrichedPATH000
getGO000
getGeneSeq000
getUniqueGOidCount000
getVennCounts000
hyperGtest000
makeVennDiagram000
mergePlusMinusPeaks0.000.020.02
myPeakList0.020.000.01
oligoFrequency0.220.020.28
oligoSummary000
peakPermTest000
peaksNearBDP0.010.000.02
pie1000
plotBinOverRegions000
preparePool000
reCenterPeaks0.050.000.04
summarizeOverlapsByBins 3.25 0.0020.06
summarizePatternInPeaks0.730.000.74
tileCount 1.21 0.0019.78
tileGRanges0.060.000.06
toGRanges0.230.000.24
translatePattern000
wgEncodeTfbsV30.050.020.06
write2FASTA0.010.000.02
xget0.130.000.12