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CHECK report for ChIPpeakAnno on merida1

This page was generated on 2020-08-11 11:52:53 -0400 (Tue, 11 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE ChIPpeakAnno PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 274/1885HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPpeakAnno 3.23.4
Lihua Julie Zhu
Snapshot Date: 2020-08-10 14:50:56 -0400 (Mon, 10 Aug 2020)
URL: https://git.bioconductor.org/packages/ChIPpeakAnno
Branch: master
Last Commit: 538e556
Last Changed Date: 2020-08-04 12:43:36 -0400 (Tue, 04 Aug 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  NA 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: ChIPpeakAnno
Version: 3.23.4
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_3.23.4.tar.gz
StartedAt: 2020-08-10 23:18:28 -0400 (Mon, 10 Aug 2020)
EndedAt: 2020-08-10 23:28:42 -0400 (Mon, 10 Aug 2020)
EllapsedTime: 613.5 seconds
RetCode: 0
Status:  OK 
CheckDir: ChIPpeakAnno.Rcheck
Warnings: 0

Command output

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### Running 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_3.23.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/ChIPpeakAnno.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-apple-darwin17.0 (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 ‘3.23.4’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 27.6Mb
  sub-directories of 1Mb or more:
    data     21.1Mb
    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 (user + system) or elapsed time > 5s
                           user system elapsed
findEnhancers            37.516  0.424  37.990
findMotifsInPromoterSeqs 20.753  0.351  21.465
annoPeaks                 3.573  0.346   5.363
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/ChIPpeakAnno.Rcheck/00check.log’
for details.



Installation output

ChIPpeakAnno.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ChIPpeakAnno
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘ChIPpeakAnno’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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: 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.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: GenomicRanges
Loading required package: GenomeInfoDb
[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: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

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 
115.339   2.572 119.436 

Example timings

ChIPpeakAnno.Rcheck/ChIPpeakAnno-Ex.timings

nameusersystemelapsed
ChIPpeakAnno-package0.0010.0000.001
ExonPlusUtr.human.GRCh372.7760.1152.895
HOT.spots0.0620.0120.073
IDRfilter0.0020.0010.003
Peaks.Ste12.Replicate10.0900.0030.093
Peaks.Ste12.Replicate20.0230.0030.025
Peaks.Ste12.Replicate30.0240.0040.029
TSS.human.GRCh370.1810.0170.199
TSS.human.GRCh380.0830.0110.094
TSS.human.NCBI360.0650.0060.071
TSS.mouse.GRCm380.0640.0040.068
TSS.mouse.NCBIM370.0570.0070.064
TSS.rat.RGSC3.40.0500.0070.057
TSS.rat.Rnor_5.00.0470.0070.054
TSS.zebrafish.Zv80.0410.0060.048
TSS.zebrafish.Zv90.1920.0170.211
addAncestors1.9320.0792.014
addGeneIDs2.4840.5313.019
addMetadata2.2390.0892.332
annoGR000
annoPeaks3.5730.3465.363
annotatePeakInBatch3.8600.1444.026
annotatedPeak0.0530.0040.057
assignChromosomeRegion0.0020.0010.003
bdp0.0010.0000.001
binOverFeature0.9290.0060.937
binOverGene0.0020.0000.003
binOverRegions0.0020.0000.003
condenseMatrixByColnames0.0180.0010.020
convert2EntrezID0.4640.0070.472
countPatternInSeqs0.2280.0050.233
cumulativePercentage0.0010.0010.000
egOrgMap0.0000.0000.001
enrichedGO0.0030.0020.004
estFragmentLength0.0010.0010.002
estLibSize0.0010.0000.001
featureAlignedDistribution0.3800.0020.383
featureAlignedExtendSignal0.0060.0010.007
featureAlignedHeatmap0.5370.0040.541
featureAlignedSignal0.3530.0790.433
findEnhancers37.516 0.42437.990
findMotifsInPromoterSeqs20.753 0.35121.465
findOverlappingPeaks0.0020.0010.004
findOverlapsOfPeaks0.8870.0110.903
getAllPeakSequence0.6850.0180.707
getAnnotation0.0010.0000.001
getEnrichedGO0.0230.0080.032
getEnrichedPATH0.0000.0010.002
getGO0.0010.0010.001
getGeneSeq0.0030.0010.004
getUniqueGOidCount0.0000.0010.002
getVennCounts0.0030.0010.004
hyperGtest0.0020.0020.003
makeVennDiagram0.0100.0020.011
mergePlusMinusPeaks0.0020.0010.003
myPeakList0.0100.0030.013
oligoFrequency0.2190.0150.234
oligoSummary0.0010.0010.002
peakPermTest0.0030.0010.004
peaksNearBDP0.0020.0000.003
pie10.0110.0000.012
plotBinOverRegions0.0020.0000.002
preparePool0.0020.0000.002
reCenterPeaks0.0360.0000.036
summarizeOverlapsByBins2.6460.3622.669
summarizePatternInPeaks0.7690.0650.834
tileCount0.5530.3160.534
tileGRanges0.0470.0060.053
toGRanges0.2790.0320.311
translatePattern0.0010.0010.001
wgEncodeTfbsV30.0670.0110.079
write2FASTA0.0210.0030.024
xget0.1220.0090.133