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CHECK report for ChIPpeakAnno on merida1

This page was generated on 2019-04-16 11:55:04 -0400 (Tue, 16 Apr 2019).

Package 246/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPpeakAnno 3.16.1
Lihua Julie Zhu
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/ChIPpeakAnno
Branch: RELEASE_3_8
Last Commit: 924626e
Last Changed Date: 2019-01-09 14:06:06 -0400 (Wed, 09 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  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: 3.16.1
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_3.16.1.tar.gz
StartedAt: 2019-04-15 22:55:04 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 23:02:43 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 458.8 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_3.16.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/ChIPpeakAnno.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘3.16.1’
* 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            18.013  0.221  18.642
ExonPlusUtr.human.GRCh37  4.859  0.133   5.077
* 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-3.8-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/3.5/Resources/library’
* installing *source* package ‘ChIPpeakAnno’ ...
** 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
* DONE (ChIPpeakAnno)

Tests output

ChIPpeakAnno.Rcheck/tests/runTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
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, colMeans, colSums, colnames,
    dirname, 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: 188 SKIPPED: 5 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 75.148   2.512  78.737 

Example timings

ChIPpeakAnno.Rcheck/ChIPpeakAnno-Ex.timings

nameusersystemelapsed
BED2RangedData0.0470.0000.048
ChIPpeakAnno-package0.0010.0000.001
ExonPlusUtr.human.GRCh374.8590.1335.077
GFF2RangedData0.0230.0010.024
HOT.spots0.2030.0480.254
IDRfilter0.0020.0000.003
Peaks.Ste12.Replicate10.3710.0080.385
Peaks.Ste12.Replicate20.1890.0080.197
Peaks.Ste12.Replicate30.1920.0180.211
TSS.human.GRCh370.2300.0440.275
TSS.human.GRCh380.7170.0150.786
TSS.human.NCBI360.2160.0410.257
TSS.mouse.GRCm380.2090.0470.257
TSS.mouse.NCBIM370.1870.0450.235
TSS.rat.RGSC3.40.1600.0420.204
TSS.rat.Rnor_5.00.1440.0420.186
TSS.zebrafish.Zv80.2660.0500.317
TSS.zebrafish.Zv90.1770.0400.275
addAncestors3.3970.1783.645
addGeneIDs2.0720.2802.442
addMetadata1.5980.1191.769
annoGR0.0010.0000.001
annoPeaks2.8030.2773.207
annotatePeakInBatch2.8750.1953.149
annotatedPeak0.1320.0080.140
assignChromosomeRegion0.0050.0000.005
bdp0.0010.0000.001
binOverFeature0.7090.0250.738
binOverGene0.0030.0000.003
binOverRegions0.0020.0010.003
condenseMatrixByColnames0.0230.0000.023
convert2EntrezID0.3910.0060.444
countPatternInSeqs0.1420.0010.150
cumulativePercentage0.0010.0010.000
egOrgMap0.0000.0000.001
enrichedGO0.0020.0020.003
estFragmentLength0.0010.0000.002
estLibSize0.0010.0010.002
featureAlignedDistribution0.3070.0010.320
featureAlignedExtentSignal0.0060.0010.006
featureAlignedHeatmap0.5490.0070.564
featureAlignedSignal0.2780.0500.328
findEnhancers18.013 0.22118.642
findOverlappingPeaks0.0010.0000.002
findOverlapsOfPeaks0.5630.0040.571
getAllPeakSequence0.4860.0210.525
getAnnotation0.0010.0000.001
getEnrichedGO0.0220.0040.025
getEnrichedPATH0.0000.0000.001
getGeneSeq0.0030.0010.003
getUniqueGOidCount0.0010.0000.001
getVennCounts0.0030.0010.003
hyperGtest0.0020.0000.002
makeVennDiagram0.0040.0010.004
mergePlusMinusPeaks0.0010.0000.001
myPeakList0.0230.0030.026
oligoFrequency0.0070.0010.008
oligoSummary0.0010.0000.000
peakPermTest0.0020.0000.002
peaksNearBDP0.0030.0000.002
pie10.0100.0010.011
plotBinOverRegions0.0010.0010.001
preparePool0.0010.0000.001
reCenterPeaks0.0140.0000.015
summarizeOverlapsByBins0.8180.5090.912
summarizePatternInPeaks0.7440.1000.852
tileCount0.6430.4830.701
tileGRanges0.0470.0180.065
toGRanges0.1110.0240.136
translatePattern0.0010.0000.001
wgEncodeTfbsV30.2880.0160.309
write2FASTA0.0190.0030.022
xget0.1200.0100.131