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CHECK report for ChIPpeakAnno on malbec1

This page was generated on 2020-04-15 12:05:36 -0400 (Wed, 15 Apr 2020).

Package 274/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPpeakAnno 3.20.1
Lihua Julie Zhu
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/ChIPpeakAnno
Branch: RELEASE_3_10
Last Commit: dcea315
Last Changed Date: 2020-02-24 11:49:25 -0400 (Mon, 24 Feb 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ChIPpeakAnno
Version: 3.20.1
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings ChIPpeakAnno_3.20.1.tar.gz
StartedAt: 2020-04-15 00:39:33 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 00:47:47 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 493.7 seconds
RetCode: 0
Status:  OK 
CheckDir: ChIPpeakAnno.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings ChIPpeakAnno_3.20.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/ChIPpeakAnno.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (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 26.24  0.024  26.295
* 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
  ‘/home/biocbuild/bbs-3.10-bioc/meat/ChIPpeakAnno.Rcheck/00check.log’
for details.



Installation output

ChIPpeakAnno.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL ChIPpeakAnno
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/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)

Tests output

ChIPpeakAnno.Rcheck/tests/runTests.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
 91.608   1.092  93.737 

Example timings

ChIPpeakAnno.Rcheck/ChIPpeakAnno-Ex.timings

nameusersystemelapsed
BED2RangedData0.0400.0000.041
ChIPpeakAnno-package000
ExonPlusUtr.human.GRCh374.0920.0724.167
GFF2RangedData0.0200.0040.022
HOT.spots0.2040.0000.205
IDRfilter0.0000.0000.002
Peaks.Ste12.Replicate10.0480.0000.047
Peaks.Ste12.Replicate20.0120.0000.012
Peaks.Ste12.Replicate30.0120.0000.012
TSS.human.GRCh370.1520.0000.152
TSS.human.GRCh380.6160.0200.636
TSS.human.NCBI360.1760.0120.190
TSS.mouse.GRCm380.2760.0000.279
TSS.mouse.NCBIM370.1280.0000.130
TSS.rat.RGSC3.40.0960.0000.094
TSS.rat.Rnor_5.00.0720.0120.087
TSS.zebrafish.Zv80.2160.0040.222
TSS.zebrafish.Zv90.1640.0080.170
addAncestors2.4800.0402.522
addGeneIDs2.0320.1322.192
addMetadata1.7360.0281.769
annoGR0.0000.0000.001
annoPeaks2.4440.1963.441
annotatePeakInBatch3.2000.0643.267
annotatedPeak0.1400.0000.141
assignChromosomeRegion0.0000.0000.002
bdp0.0000.0000.001
binOverFeature1.1000.0161.118
binOverGene0.0000.0000.002
binOverRegions0.0040.0000.001
condenseMatrixByColnames0.0200.0000.022
convert2EntrezID0.3640.0000.367
countPatternInSeqs0.1520.0000.154
cumulativePercentage0.0000.0000.001
egOrgMap0.0000.0000.001
enrichedGO0.0040.0000.003
estFragmentLength000
estLibSize0.0000.0000.001
featureAlignedDistribution0.3320.0000.333
featureAlignedExtentSignal0.0040.0000.003
featureAlignedHeatmap0.780.000.78
featureAlignedSignal0.2760.0280.307
findEnhancers26.240 0.02426.295
findOverlappingPeaks0.0000.0000.001
findOverlapsOfPeaks0.5600.0040.598
getAllPeakSequence0.7440.0121.379
getAnnotation0.0000.0000.001
getEnrichedGO0.0200.0000.018
getEnrichedPATH000
getGeneSeq0.0000.0000.003
getUniqueGOidCount0.0040.0000.001
getVennCounts0.0040.0000.002
hyperGtest0.0000.0000.001
makeVennDiagram0.0000.0040.006
mergePlusMinusPeaks0.0040.0000.001
myPeakList0.0280.0000.029
oligoFrequency0.0080.0040.011
oligoSummary000
peakPermTest0.0000.0000.002
peaksNearBDP0.0000.0000.001
pie10.0080.0040.012
plotBinOverRegions0.0040.0000.001
preparePool0.0000.0000.001
reCenterPeaks0.0400.0000.041
summarizeOverlapsByBins3.1480.8683.780
summarizePatternInPeaks0.7840.0320.816
tileCount0.2760.1600.399
tileGRanges0.1880.0720.037
toGRanges0.1600.0040.166
translatePattern000
wgEncodeTfbsV30.2280.0000.229
write2FASTA0.0120.0040.014
xget0.1120.0040.115