Package: ChIPpeakAnno

Version: 3.12.7

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ChIPpeakAnno_3.12.7.tar.gz

StartedAt: 2018-04-12 01:34:08 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 01:41:06 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 417.5 seconds

RetCode: 0

Status:  OK

CheckDir: ChIPpeakAnno.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ChIPpeakAnno_3.12.7.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/ChIPpeakAnno.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘3.12.7’
* 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 24.1Mb
  sub-directories of 1Mb or more:
    data     12.7Mb
    doc       5.6Mb
    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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
findEnhancers            20.044  0.174  20.689
ExonPlusUtr.human.GRCh37  4.977  0.118   5.197
* 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-3.6-bioc/meat/ChIPpeakAnno.Rcheck/00check.log’
for details.

* installing *source* package ‘ChIPpeakAnno’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ChIPpeakAnno)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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, cbind, colMeans, colSums, colnames, 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: 192 SKIPPED: 4 FAILED: 0
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
 69.623   1.655  73.645 

name	user	system	elapsed
BED2RangedData	0.195	0.011	0.213
ChIPpeakAnno-package	0.001	0.000	0.002
ExonPlusUtr.human.GRCh37	4.977	0.118	5.197
GFF2RangedData	0.169	0.002	0.173
HOT.spots	0.145	0.030	0.180
IDRfilter	0.001	0.000	0.001
Peaks.Ste12.Replicate1	0.030	0.003	0.034
Peaks.Ste12.Replicate2	0.023	0.003	0.027
Peaks.Ste12.Replicate3	0.030	0.003	0.034
TSS.human.GRCh37	0.143	0.026	0.174
TSS.human.GRCh38	0.699	0.012	0.720
TSS.human.NCBI36	0.153	0.030	0.184
TSS.mouse.GRCm38	0.243	0.031	0.279
TSS.mouse.NCBIM37	0.128	0.026	0.157
TSS.rat.RGSC3.4	0.105	0.031	0.136
TSS.rat.Rnor_5.0	0.630	0.033	0.671
TSS.zebrafish.Zv8	0.088	0.028	0.117
TSS.zebrafish.Zv9	0.106	0.028	0.136
addAncestors	1.575	0.095	1.695
addGeneIDs	1.636	0.114	1.768
addMetadata	1.891	0.083	2.008
annoGR	0.001	0.000	0.001
annoPeaks	2.741	0.215	3.014
annotatePeakInBatch	3.098	0.144	3.293
annotatedPeak	0.114	0.008	0.124
assignChromosomeRegion	0.006	0.001	0.006
bdp	0.001	0.000	0.001
binOverFeature	1.200	0.031	1.254
binOverGene	0.003	0.001	0.003
binOverRegions	0.003	0.000	0.003
condenseMatrixByColnames	0.057	0.001	0.059
convert2EntrezID	0.399	0.005	0.415
countPatternInSeqs	0.294	0.002	0.302
cumulativePercentage	0.001	0.000	0.001
egOrgMap	0.02	0.00	0.02
enrichedGO	0.003	0.001	0.005
estFragmentLength	0.002	0.000	0.002
estLibSize	0.002	0.000	0.002
featureAlignedDistribution	0.471	0.004	0.481
featureAlignedExtentSignal	0.005	0.000	0.005
featureAlignedHeatmap	0.638	0.002	0.644
featureAlignedSignal	0.198	0.029	0.237
findEnhancers	20.044	0.174	20.689
findOverlappingPeaks	0.004	0.001	0.004
findOverlapsOfPeaks	1.267	0.005	1.317
getAllPeakSequence	0.703	0.021	0.749
getAnnotation	0.001	0.000	0.001
getEnrichedGO	0.019	0.002	0.021
getEnrichedPATH	0.002	0.001	0.002
getGeneSeq	0.006	0.000	0.006
getUniqueGOidCount	0.001	0.000	0.002
getVennCounts	0.003	0.000	0.005
hyperGtest	0.02	0.00	0.02
makeVennDiagram	0.006	0.000	0.006
mergePlusMinusPeaks	0.003	0.000	0.003
myPeakList	0.020	0.004	0.024
oligoFrequency	0.028	0.002	0.031
oligoSummary	0.002	0.001	0.001
peakPermTest	0.002	0.000	0.003
peaksNearBDP	0.002	0.000	0.002
pie1	0.009	0.000	0.010
plotBinOverRegions	0.003	0.001	0.003
preparePool	0.002	0.000	0.002
reCenterPeaks	0.018	0.000	0.019
summarizeOverlapsByBins	0.495	0.150	1.109
summarizePatternInPeaks	0.909	0.079	1.006
tileCount	0.599	0.201	1.106
tileGRanges	0.044	0.019	0.063
toGRanges	0.101	0.014	0.116
translatePattern	0.001	0.001	0.001
wgEncodeTfbsV3	0.230	0.014	0.245
write2FASTA	0.042	0.007	0.050
xget	0.144	0.007	0.151