Package: ChIPpeakAnno

Version: 3.14.2

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_3.14.2.tar.gz

StartedAt: 2018-10-16 20:24:12 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 20:32:00 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 467.8 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_3.14.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/ChIPpeakAnno.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘3.14.2’
* 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 17.652  0.216  18.008
* 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-3.7-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 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
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, 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 
 83.527   2.448  87.634 

name	user	system	elapsed
BED2RangedData	0.050	0.001	0.051
ChIPpeakAnno-package	0.003	0.000	0.003
ExonPlusUtr.human.GRCh37	3.937	0.121	4.081
GFF2RangedData	0.017	0.000	0.017
HOT.spots	0.164	0.037	0.202
IDRfilter	0.003	0.000	0.002
Peaks.Ste12.Replicate1	0.394	0.006	0.407
Peaks.Ste12.Replicate2	0.150	0.007	0.158
Peaks.Ste12.Replicate3	0.190	0.022	0.214
TSS.human.GRCh37	0.289	0.034	0.324
TSS.human.GRCh38	0.661	0.010	0.681
TSS.human.NCBI36	0.917	0.040	0.963
TSS.mouse.GRCm38	0.160	0.037	0.198
TSS.mouse.NCBIM37	0.139	0.037	0.175
TSS.rat.RGSC3.4	0.108	0.036	0.144
TSS.rat.Rnor_5.0	0.115	0.039	0.154
TSS.zebrafish.Zv8	0.109	0.041	0.149
TSS.zebrafish.Zv9	0.134	0.035	0.172
addAncestors	2.072	0.140	2.232
addGeneIDs	1.800	0.259	2.080
addMetadata	1.367	0.094	1.474
annoGR	0.002	0.000	0.002
annoPeaks	2.461	0.249	2.759
annotatePeakInBatch	2.744	0.200	2.978
annotatedPeak	0.107	0.006	0.116
assignChromosomeRegion	0.007	0.001	0.008
bdp	0.002	0.000	0.002
binOverFeature	0.625	0.024	0.653
binOverGene	0.004	0.000	0.005
binOverRegions	0.004	0.000	0.005
condenseMatrixByColnames	0.018	0.000	0.018
convert2EntrezID	0.300	0.006	0.307
countPatternInSeqs	0.119	0.002	0.121
cumulativePercentage	0.001	0.000	0.002
egOrgMap	0.002	0.001	0.002
enrichedGO	0.005	0.002	0.007
estFragmentLength	0.002	0.001	0.003
estLibSize	0.003	0.000	0.003
featureAlignedDistribution	0.307	0.003	0.314
featureAlignedExtentSignal	0.01	0.00	0.01
featureAlignedHeatmap	0.497	0.010	0.511
featureAlignedSignal	0.237	0.035	0.274
findEnhancers	17.652	0.216	18.008
findOverlappingPeaks	0.003	0.000	0.003
findOverlapsOfPeaks	0.531	0.004	0.543
getAllPeakSequence	0.547	0.019	0.570
getAnnotation	0.002	0.000	0.003
getEnrichedGO	0.019	0.003	0.024
getEnrichedPATH	0.002	0.000	0.002
getGeneSeq	0.005	0.000	0.006
getUniqueGOidCount	0.002	0.001	0.002
getVennCounts	0.003	0.000	0.003
hyperGtest	0.003	0.000	0.003
makeVennDiagram	0.006	0.000	0.007
mergePlusMinusPeaks	0.004	0.000	0.005
myPeakList	0.025	0.003	0.028
oligoFrequency	0.012	0.003	0.015
oligoSummary	0.003	0.000	0.004
peakPermTest	0.003	0.001	0.003
peaksNearBDP	0.003	0.000	0.003
pie1	0.011	0.001	0.012
plotBinOverRegions	0.005	0.000	0.005
preparePool	0.002	0.000	0.002
reCenterPeaks	0.023	0.000	0.024
summarizeOverlapsByBins	0.914	0.650	1.084
summarizePatternInPeaks	0.700	0.089	0.793
tileCount	0.607	0.449	0.664
tileGRanges	0.055	0.022	0.078
toGRanges	0.115	0.022	0.138
translatePattern	0.002	0.000	0.002
wgEncodeTfbsV3	0.264	0.014	0.279
write2FASTA	0.013	0.001	0.015
xget	0.108	0.011	0.120