Package: ChIPpeakAnno

Version: 3.18.2

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_3.18.2.tar.gz

StartedAt: 2019-10-16 01:23:16 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 01:33:41 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 625.5 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_3.18.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/ChIPpeakAnno.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘3.18.2’
* 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           21.081  0.387  21.634
summarizeOverlapsByBins  4.396  0.897   4.627
* 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’ ...
** 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 3.6.1 (2019-07-05) -- "Action of the Toes"
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, 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: 187 | SKIPPED: 5 | WARNINGS: 6 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 99.168   5.408 105.318 

name	user	system	elapsed
BED2RangedData	0.080	0.006	0.087
ChIPpeakAnno-package	0.001	0.000	0.002
ExonPlusUtr.human.GRCh37	4.157	0.223	4.380
GFF2RangedData	0.025	0.001	0.026
HOT.spots	0.189	0.059	0.248
IDRfilter	0.001	0.000	0.002
Peaks.Ste12.Replicate1	0.317	0.004	0.321
Peaks.Ste12.Replicate2	0.217	0.006	0.222
Peaks.Ste12.Replicate3	0.236	0.005	0.240
TSS.human.GRCh37	0.212	0.054	0.265
TSS.human.GRCh38	0.706	0.023	0.728
TSS.human.NCBI36	0.215	0.057	0.271
TSS.mouse.GRCm38	0.382	0.063	0.445
TSS.mouse.NCBIM37	0.168	0.059	0.227
TSS.rat.RGSC3.4	0.160	0.064	0.224
TSS.rat.Rnor_5.0	0.117	0.061	0.179
TSS.zebrafish.Zv8	0.145	0.068	0.214
TSS.zebrafish.Zv9	0.180	0.065	0.245
addAncestors	3.648	0.259	3.907
addGeneIDs	2.372	0.474	2.853
addMetadata	1.994	0.279	2.273
annoGR	0.001	0.000	0.001
annoPeaks	2.976	0.682	3.890
annotatePeakInBatch	3.326	0.362	3.779
annotatedPeak	0.123	0.013	0.137
assignChromosomeRegion	0.005	0.001	0.006
bdp	0.000	0.000	0.001
binOverFeature	0.966	0.046	1.014
binOverGene	0.001	0.001	0.002
binOverRegions	0.003	0.001	0.002
condenseMatrixByColnames	0.027	0.001	0.028
convert2EntrezID	0.369	0.008	0.377
countPatternInSeqs	0.145	0.002	0.148
cumulativePercentage	0.000	0.001	0.001
egOrgMap	0.000	0.000	0.001
enrichedGO	0.003	0.002	0.005
estFragmentLength	0.002	0.001	0.002
estLibSize	0.002	0.001	0.002
featureAlignedDistribution	0.548	0.041	0.589
featureAlignedExtentSignal	0.007	0.001	0.007
featureAlignedHeatmap	0.555	0.014	0.569
featureAlignedSignal	0.292	0.081	0.373
findEnhancers	21.081	0.387	21.634
findOverlappingPeaks	0.004	0.001	0.003
findOverlapsOfPeaks	0.427	0.007	0.434
getAllPeakSequence	0.698	0.031	0.740
getAnnotation	0.001	0.001	0.000
getEnrichedGO	0.029	0.007	0.036
getEnrichedPATH	0.001	0.001	0.001
getGeneSeq	0.005	0.001	0.006
getUniqueGOidCount	0.001	0.001	0.003
getVennCounts	0.003	0.001	0.004
hyperGtest	0.003	0.001	0.003
makeVennDiagram	0.008	0.001	0.008
mergePlusMinusPeaks	0.003	0.001	0.003
myPeakList	0.026	0.008	0.033
oligoFrequency	0.014	0.006	0.020
oligoSummary	0.001	0.000	0.001
peakPermTest	0.002	0.001	0.003
peaksNearBDP	0.002	0.001	0.003
pie1	0.012	0.001	0.015
plotBinOverRegions	0.001	0.000	0.002
preparePool	0.001	0.001	0.001
reCenterPeaks	0.022	0.000	0.022
summarizeOverlapsByBins	4.396	0.897	4.627
summarizePatternInPeaks	0.849	0.143	0.992
tileCount	2.013	1.141	2.581
tileGRanges	0.055	0.033	0.089
toGRanges	0.381	0.078	0.459
translatePattern	0.001	0.002	0.003
wgEncodeTfbsV3	0.296	0.033	0.329
write2FASTA	0.024	0.008	0.031
xget	0.144	0.015	0.160