Package: ChIPpeakAnno

Version: 3.17.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ChIPpeakAnno_3.17.2.tar.gz

StartedAt: 2019-04-08 23:49:56 -0400 (Mon, 08 Apr 2019)

EndedAt: 2019-04-08 23:57:42 -0400 (Mon, 08 Apr 2019)

EllapsedTime: 465.7 seconds

RetCode: 0

Status:  OK

CheckDir: ChIPpeakAnno.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ChIPpeakAnno_3.17.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/ChIPpeakAnno.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChIPpeakAnno/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChIPpeakAnno’ version ‘3.17.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'grid', 'IRanges', 'Biostrings', 'GenomicRanges', 'S4Vectors',
  'VennDiagram'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ChIPpeakAnno’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 19.0Mb
  sub-directories of 1Mb or more:
    data     12.6Mb
    extdata   5.2Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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 ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
findEnhancers 17.84  0.181  18.211
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/ChIPpeakAnno.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ChIPpeakAnno
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘ChIPpeakAnno’ ...
** R
** data
** 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
* DONE (ChIPpeakAnno)

R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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: grid
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, colMeans, colSums, 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, rowMeans, rowSums,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, 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

Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: VennDiagram
Loading required package: futile.logger

[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: 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: 193 SKIPPED: 5 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 77.291   2.510  80.761 

name	user	system	elapsed
BED2RangedData	0.051	0.000	0.051
ChIPpeakAnno-package	0.001	0.000	0.001
ExonPlusUtr.human.GRCh37	3.727	0.126	3.880
GFF2RangedData	0.015	0.000	0.016
HOT.spots	0.174	0.039	0.214
IDRfilter	0.001	0.000	0.002
Peaks.Ste12.Replicate1	0.329	0.006	0.337
Peaks.Ste12.Replicate2	0.169	0.004	0.173
Peaks.Ste12.Replicate3	0.148	0.021	0.173
TSS.human.GRCh37	0.202	0.035	0.241
TSS.human.GRCh38	0.646	0.013	0.665
TSS.human.NCBI36	0.196	0.041	0.237
TSS.mouse.GRCm38	0.174	0.040	0.218
TSS.mouse.NCBIM37	0.154	0.039	0.196
TSS.rat.RGSC3.4	0.218	0.042	0.262
TSS.rat.Rnor_5.0	0.109	0.034	0.142
TSS.zebrafish.Zv8	0.126	0.036	0.165
TSS.zebrafish.Zv9	0.156	0.036	0.194
addAncestors	2.907	0.129	3.076
addGeneIDs	1.853	0.241	2.125
addMetadata	1.272	0.077	1.359
annoGR	0.001	0.000	0.001
annoPeaks	2.314	0.259	2.624
annotatePeakInBatch	2.559	0.179	2.759
annotatedPeak	0.128	0.004	0.134
assignChromosomeRegion	0.005	0.000	0.005
bdp	0.001	0.000	0.001
binOverFeature	0.900	0.026	0.947
binOverGene	0.002	0.000	0.002
binOverRegions	0.003	0.001	0.003
condenseMatrixByColnames	0.018	0.000	0.019
convert2EntrezID	0.346	0.006	0.354
countPatternInSeqs	0.139	0.000	0.142
cumulativePercentage	0.001	0.000	0.000
egOrgMap	0.000	0.000	0.001
enrichedGO	0.004	0.002	0.006
estFragmentLength	0.001	0.000	0.001
estLibSize	0.002	0.000	0.002
featureAlignedDistribution	0.243	0.001	0.251
featureAlignedExtentSignal	0.003	0.001	0.003
featureAlignedHeatmap	0.461	0.004	0.470
featureAlignedSignal	0.193	0.041	0.236
findEnhancers	17.840	0.181	18.211
findOverlappingPeaks	0.003	0.001	0.004
findOverlapsOfPeaks	0.616	0.005	0.635
getAllPeakSequence	0.572	0.023	0.608
getAnnotation	0.001	0.000	0.001
getEnrichedGO	0.021	0.002	0.023
getEnrichedPATH	0.001	0.000	0.002
getGeneSeq	0.005	0.001	0.006
getUniqueGOidCount	0.002	0.000	0.001
getVennCounts	0.003	0.001	0.003
hyperGtest	0.002	0.000	0.002
makeVennDiagram	0.005	0.000	0.004
mergePlusMinusPeaks	0.002	0.000	0.002
myPeakList	0.018	0.002	0.020
oligoFrequency	0.007	0.001	0.010
oligoSummary	0.001	0.000	0.000
peakPermTest	0.001	0.000	0.002
peaksNearBDP	0.001	0.000	0.001
pie1	0.010	0.000	0.011
plotBinOverRegions	0.003	0.001	0.003
preparePool	0.002	0.000	0.001
reCenterPeaks	0.021	0.001	0.021
summarizeOverlapsByBins	0.876	0.611	1.007
summarizePatternInPeaks	0.633	0.070	0.706
tileCount	0.568	0.352	0.545
tileGRanges	0.045	0.023	0.068
toGRanges	0.338	0.068	0.410
translatePattern	0.001	0.001	0.001
wgEncodeTfbsV3	0.255	0.016	0.271
write2FASTA	0.018	0.002	0.020
xget	0.102	0.007	0.110