Package: ChIPpeakAnno

Version: 3.16.1

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_3.16.1.tar.gz

StartedAt: 2019-04-15 22:55:04 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-15 23:02:43 -0400 (Mon, 15 Apr 2019)

EllapsedTime: 458.8 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_3.16.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/ChIPpeakAnno.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘3.16.1’
* 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            18.013  0.221  18.642
ExonPlusUtr.human.GRCh37  4.859  0.133   5.077
* 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-3.8-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/3.5/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 version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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, lengths, 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: 188 SKIPPED: 5 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 75.148   2.512  78.737 

name	user	system	elapsed
BED2RangedData	0.047	0.000	0.048
ChIPpeakAnno-package	0.001	0.000	0.001
ExonPlusUtr.human.GRCh37	4.859	0.133	5.077
GFF2RangedData	0.023	0.001	0.024
HOT.spots	0.203	0.048	0.254
IDRfilter	0.002	0.000	0.003
Peaks.Ste12.Replicate1	0.371	0.008	0.385
Peaks.Ste12.Replicate2	0.189	0.008	0.197
Peaks.Ste12.Replicate3	0.192	0.018	0.211
TSS.human.GRCh37	0.230	0.044	0.275
TSS.human.GRCh38	0.717	0.015	0.786
TSS.human.NCBI36	0.216	0.041	0.257
TSS.mouse.GRCm38	0.209	0.047	0.257
TSS.mouse.NCBIM37	0.187	0.045	0.235
TSS.rat.RGSC3.4	0.160	0.042	0.204
TSS.rat.Rnor_5.0	0.144	0.042	0.186
TSS.zebrafish.Zv8	0.266	0.050	0.317
TSS.zebrafish.Zv9	0.177	0.040	0.275
addAncestors	3.397	0.178	3.645
addGeneIDs	2.072	0.280	2.442
addMetadata	1.598	0.119	1.769
annoGR	0.001	0.000	0.001
annoPeaks	2.803	0.277	3.207
annotatePeakInBatch	2.875	0.195	3.149
annotatedPeak	0.132	0.008	0.140
assignChromosomeRegion	0.005	0.000	0.005
bdp	0.001	0.000	0.001
binOverFeature	0.709	0.025	0.738
binOverGene	0.003	0.000	0.003
binOverRegions	0.002	0.001	0.003
condenseMatrixByColnames	0.023	0.000	0.023
convert2EntrezID	0.391	0.006	0.444
countPatternInSeqs	0.142	0.001	0.150
cumulativePercentage	0.001	0.001	0.000
egOrgMap	0.000	0.000	0.001
enrichedGO	0.002	0.002	0.003
estFragmentLength	0.001	0.000	0.002
estLibSize	0.001	0.001	0.002
featureAlignedDistribution	0.307	0.001	0.320
featureAlignedExtentSignal	0.006	0.001	0.006
featureAlignedHeatmap	0.549	0.007	0.564
featureAlignedSignal	0.278	0.050	0.328
findEnhancers	18.013	0.221	18.642
findOverlappingPeaks	0.001	0.000	0.002
findOverlapsOfPeaks	0.563	0.004	0.571
getAllPeakSequence	0.486	0.021	0.525
getAnnotation	0.001	0.000	0.001
getEnrichedGO	0.022	0.004	0.025
getEnrichedPATH	0.000	0.000	0.001
getGeneSeq	0.003	0.001	0.003
getUniqueGOidCount	0.001	0.000	0.001
getVennCounts	0.003	0.001	0.003
hyperGtest	0.002	0.000	0.002
makeVennDiagram	0.004	0.001	0.004
mergePlusMinusPeaks	0.001	0.000	0.001
myPeakList	0.023	0.003	0.026
oligoFrequency	0.007	0.001	0.008
oligoSummary	0.001	0.000	0.000
peakPermTest	0.002	0.000	0.002
peaksNearBDP	0.003	0.000	0.002
pie1	0.010	0.001	0.011
plotBinOverRegions	0.001	0.001	0.001
preparePool	0.001	0.000	0.001
reCenterPeaks	0.014	0.000	0.015
summarizeOverlapsByBins	0.818	0.509	0.912
summarizePatternInPeaks	0.744	0.100	0.852
tileCount	0.643	0.483	0.701
tileGRanges	0.047	0.018	0.065
toGRanges	0.111	0.024	0.136
translatePattern	0.001	0.000	0.001
wgEncodeTfbsV3	0.288	0.016	0.309
write2FASTA	0.019	0.003	0.022
xget	0.120	0.010	0.131