Package: ChIPpeakAnno

Version: 3.20.1

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_3.20.1.tar.gz

StartedAt: 2020-04-15 01:06:45 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 01:15:44 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 539.1 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_3.20.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/ChIPpeakAnno.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘3.20.1’
* 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 25.786  0.309  26.365
* 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-3.10-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’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ChIPpeakAnno)

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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, 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, 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: 186 | SKIPPED: 5 | WARNINGS: 1 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
103.605   2.689 107.537 

name	user	system	elapsed
BED2RangedData	0.071	0.001	0.073
ChIPpeakAnno-package	0.000	0.000	0.001
ExonPlusUtr.human.GRCh37	3.802	0.122	3.968
GFF2RangedData	0.023	0.001	0.025
HOT.spots	0.175	0.040	0.218
IDRfilter	0.003	0.000	0.003
Peaks.Ste12.Replicate1	0.043	0.036	0.079
Peaks.Ste12.Replicate2	0.014	0.029	0.043
Peaks.Ste12.Replicate3	0.015	0.030	0.045
TSS.human.GRCh37	0.165	0.036	0.206
TSS.human.GRCh38	0.582	0.011	0.594
TSS.human.NCBI36	0.152	0.039	0.191
TSS.mouse.GRCm38	0.206	0.042	0.249
TSS.mouse.NCBIM37	0.112	0.036	0.148
TSS.rat.RGSC3.4	0.100	0.034	0.134
TSS.rat.Rnor_5.0	0.087	0.035	0.126
TSS.zebrafish.Zv8	0.220	0.034	0.254
TSS.zebrafish.Zv9	0.133	0.034	0.167
addAncestors	2.282	0.095	2.387
addGeneIDs	1.718	0.234	1.975
addMetadata	1.525	0.059	1.594
annoGR	0.000	0.000	0.001
annoPeaks	2.206	0.283	2.635
annotatePeakInBatch	2.774	0.186	2.979
annotatedPeak	0.092	0.005	0.097
assignChromosomeRegion	0.004	0.000	0.004
bdp	0.001	0.000	0.001
binOverFeature	0.977	0.040	1.026
binOverGene	0.002	0.001	0.003
binOverRegions	0.002	0.000	0.002
condenseMatrixByColnames	0.018	0.001	0.020
convert2EntrezID	0.267	0.007	0.275
countPatternInSeqs	0.124	0.001	0.127
cumulativePercentage	0.001	0.000	0.001
egOrgMap	0.001	0.000	0.000
enrichedGO	0.003	0.001	0.003
estFragmentLength	0.001	0.000	0.001
estLibSize	0.001	0.000	0.001
featureAlignedDistribution	0.270	0.002	0.275
featureAlignedExtentSignal	0.005	0.000	0.005
featureAlignedHeatmap	0.684	0.015	0.704
featureAlignedSignal	0.198	0.028	0.226
findEnhancers	25.786	0.309	26.365
findOverlappingPeaks	0.003	0.000	0.003
findOverlapsOfPeaks	0.711	0.004	0.727
getAllPeakSequence	0.661	0.021	0.689
getAnnotation	0.001	0.000	0.001
getEnrichedGO	0.020	0.004	0.024
getEnrichedPATH	0.001	0.000	0.001
getGeneSeq	0.004	0.000	0.004
getUniqueGOidCount	0.001	0.000	0.001
getVennCounts	0.002	0.000	0.003
hyperGtest	0.002	0.001	0.002
makeVennDiagram	0.006	0.000	0.007
mergePlusMinusPeaks	0.002	0.000	0.001
myPeakList	0.018	0.002	0.020
oligoFrequency	0.011	0.003	0.015
oligoSummary	0.001	0.000	0.001
peakPermTest	0.002	0.000	0.003
peaksNearBDP	0.002	0.000	0.003
pie1	0.011	0.000	0.012
plotBinOverRegions	0.002	0.000	0.002
preparePool	0.001	0.000	0.002
reCenterPeaks	0.026	0.001	0.025
summarizeOverlapsByBins	2.488	0.377	2.547
summarizePatternInPeaks	0.791	0.086	0.908
tileCount	0.552	0.287	0.547
tileGRanges	0.052	0.007	0.060
toGRanges	0.213	0.027	0.242
translatePattern	0.000	0.000	0.001
wgEncodeTfbsV3	0.248	0.015	0.266
write2FASTA	0.022	0.002	0.025
xget	0.078	0.006	0.085