Back to Multiple platform build/check report for BioC 3.11
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for ChIPpeakAnno on celaya2

This page was generated on 2020-01-16 13:32:06 -0500 (Thu, 16 Jan 2020).

Package 274/1818HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPpeakAnno 3.21.2
Lihua Julie Zhu
Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020)
URL: https://git.bioconductor.org/packages/ChIPpeakAnno
Branch: master
Last Commit: 78fb465
Last Changed Date: 2019-12-13 11:00:48 -0500 (Fri, 13 Dec 2019)
malbec2 Linux (Ubuntu 18.04.3 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: ChIPpeakAnno
Version: 3.21.2
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_3.21.2.tar.gz
StartedAt: 2020-01-16 02:45:43 -0500 (Thu, 16 Jan 2020)
EndedAt: 2020-01-16 02:59:33 -0500 (Thu, 16 Jan 2020)
EllapsedTime: 829.9 seconds
RetCode: 0
Status:  OK 
CheckDir: ChIPpeakAnno.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_3.21.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/ChIPpeakAnno.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘3.21.2’
* 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 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 (user + system) or elapsed time > 5s
                           user system elapsed
findEnhancers            41.317  0.543  42.059
ExonPlusUtr.human.GRCh37  4.940  0.317   5.265
annotatePeakInBatch       4.793  0.388   5.188
* 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-3.11-bioc/meat/ChIPpeakAnno.Rcheck/00check.log’
for details.



Installation output

ChIPpeakAnno.Rcheck/00install.out

##############################################################################
##############################################################################
###
### 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
** 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 Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
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: 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

[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: 185 | SKIPPED: 5 | WARNINGS: 1 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
148.273   6.336 163.688 

Example timings

ChIPpeakAnno.Rcheck/ChIPpeakAnno-Ex.timings

nameusersystemelapsed
ChIPpeakAnno-package0.0010.0000.002
ExonPlusUtr.human.GRCh374.9400.3175.265
HOT.spots0.2060.0780.286
IDRfilter0.0020.0000.001
Peaks.Ste12.Replicate10.0930.0620.320
Peaks.Ste12.Replicate20.0330.0630.095
Peaks.Ste12.Replicate30.0320.0590.090
TSS.human.GRCh370.2340.0650.300
TSS.human.GRCh380.8850.0270.913
TSS.human.NCBI360.2350.0680.303
TSS.mouse.GRCm380.2240.0710.295
TSS.mouse.NCBIM370.3590.0730.431
TSS.rat.RGSC3.40.150.060.21
TSS.rat.Rnor_5.00.1390.0570.196
TSS.zebrafish.Zv80.1480.0600.208
TSS.zebrafish.Zv90.1850.0610.246
addAncestors4.2580.3224.584
addGeneIDs3.1000.7063.844
addMetadata2.7540.2923.046
annoGR0.0010.0000.001
annoPeaks3.6440.7324.721
annotatePeakInBatch4.7930.3885.188
annotatedPeak0.1370.0130.150
assignChromosomeRegion0.0050.0010.006
bdp0.0010.0000.001
binOverFeature1.5730.0631.745
binOverGene0.0020.0010.003
binOverRegions0.0020.0010.002
condenseMatrixByColnames0.0290.0010.030
convert2EntrezID0.4520.0130.469
countPatternInSeqs0.1960.0040.201
cumulativePercentage000
egOrgMap0.0010.0010.002
enrichedGO0.0040.0030.008
estFragmentLength0.0010.0000.002
estLibSize0.0010.0000.001
featureAlignedDistribution0.4820.0020.486
featureAlignedExtentSignal0.0030.0010.005
featureAlignedHeatmap0.7340.0110.746
featureAlignedSignal0.4470.0770.524
findEnhancers41.317 0.54342.059
findOverlappingPeaks0.0020.0000.002
findOverlapsOfPeaks1.0300.0111.048
getAllPeakSequence0.8460.0480.901
getAnnotation0.0000.0010.001
getEnrichedGO0.0280.0070.034
getEnrichedPATH0.0010.0000.001
getGO0.0000.0000.001
getGeneSeq0.0040.0000.004
getUniqueGOidCount0.0020.0000.002
getVennCounts0.0020.0000.002
hyperGtest0.0030.0010.003
makeVennDiagram0.0050.0010.006
mergePlusMinusPeaks0.0010.0000.002
myPeakList0.0260.0050.032
oligoFrequency0.0160.0060.020
oligoSummary0.0010.0010.001
peakPermTest0.0020.0010.002
peaksNearBDP0.0030.0010.003
pie10.0120.0010.013
plotBinOverRegions0.0020.0000.003
preparePool0.0020.0000.003
reCenterPeaks0.0500.0010.051
summarizeOverlapsByBins3.5650.8493.837
summarizePatternInPeaks1.0890.1781.267
tileCount0.9120.6460.936
tileGRanges0.1000.0180.119
toGRanges0.4540.0780.535
translatePattern0.0020.0010.002
wgEncodeTfbsV30.3550.0610.744
write2FASTA0.0530.0150.124
xget0.2340.0440.425