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CHECK report for ChIPpeakAnno on malbec1

This page was generated on 2018-04-12 13:08:46 -0400 (Thu, 12 Apr 2018).

Package 219/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPpeakAnno 3.12.7
Lihua Julie Zhu
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/ChIPpeakAnno
Branch: RELEASE_3_6
Last Commit: 2f73a77
Last Changed Date: 2018-02-15 13:40:03 -0400 (Thu, 15 Feb 2018)
malbec1 Linux (Ubuntu 16.04.1 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
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ChIPpeakAnno
Version: 3.12.7
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings ChIPpeakAnno_3.12.7.tar.gz
StartedAt: 2018-04-11 22:09:38 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 22:15:37 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 359.4 seconds
RetCode: 0
Status:  OK 
CheckDir: ChIPpeakAnno.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings ChIPpeakAnno_3.12.7.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/ChIPpeakAnno.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘3.12.7’
* 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 22.5Mb
  sub-directories of 1Mb or more:
    data     12.7Mb
    doc       4.0Mb
    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 16.296  0.044  16.364
* 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-3.6-bioc/meat/ChIPpeakAnno.Rcheck/00check.log’
for details.



Installation output

ChIPpeakAnno.Rcheck/00install.out

* 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)

Tests output

ChIPpeakAnno.Rcheck/tests/runTests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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, 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 
 59.568   0.640  61.696 

Example timings

ChIPpeakAnno.Rcheck/ChIPpeakAnno-Ex.timings

nameusersystemelapsed
BED2RangedData0.1360.0000.135
ChIPpeakAnno-package0.0000.0000.001
ExonPlusUtr.human.GRCh374.1440.0324.178
GFF2RangedData0.1200.0000.122
HOT.spots0.1360.0080.146
IDRfilter0.0000.0000.001
Peaks.Ste12.Replicate10.0600.0040.066
Peaks.Ste12.Replicate20.0200.0000.023
Peaks.Ste12.Replicate30.0200.0000.023
TSS.human.GRCh370.1240.0040.132
TSS.human.GRCh381.2880.0321.321
TSS.human.NCBI360.1800.0120.191
TSS.mouse.GRCm380.1840.0040.185
TSS.mouse.NCBIM370.1440.0000.145
TSS.rat.RGSC3.40.0960.0080.106
TSS.rat.Rnor_5.00.0800.0080.090
TSS.zebrafish.Zv80.0880.0000.088
TSS.zebrafish.Zv90.1000.0080.107
addAncestors2.4320.0682.524
addGeneIDs1.2640.0921.370
addMetadata1.5600.0121.572
annoGR0.0000.0000.001
annoPeaks3.0920.0963.823
annotatePeakInBatch2.5920.0522.644
annotatedPeak0.1000.0040.102
assignChromosomeRegion0.0040.0000.002
bdp0.0000.0000.001
binOverFeature1.0920.0041.094
binOverGene0.0000.0000.001
binOverRegions0.0000.0000.001
condenseMatrixByColnames0.0520.0000.051
convert2EntrezID0.3640.0000.365
countPatternInSeqs0.2280.0000.228
cumulativePercentage000
egOrgMap0.0160.0000.014
enrichedGO0.0040.0000.002
estFragmentLength0.0000.0000.001
estLibSize0.0040.0000.000
featureAlignedDistribution0.3600.0000.361
featureAlignedExtentSignal0.0040.0000.003
featureAlignedHeatmap0.80.00.8
featureAlignedSignal0.1440.0120.158
findEnhancers16.296 0.04416.364
findOverlappingPeaks0.0000.0000.002
findOverlapsOfPeaks1.2280.0001.275
getAllPeakSequence0.7760.0081.252
getAnnotation000
getEnrichedGO0.0120.0000.012
getEnrichedPATH0.0000.0000.001
getGeneSeq0.0000.0000.002
getUniqueGOidCount0.0040.0000.002
getVennCounts0.0000.0000.001
hyperGtest0.0120.0000.014
makeVennDiagram0.0040.0000.003
mergePlusMinusPeaks0.0040.0000.002
myPeakList0.0160.0000.017
oligoFrequency0.020.000.02
oligoSummary0.0000.0000.001
peakPermTest0.0040.0000.002
peaksNearBDP0.0000.0000.001
pie10.0080.0000.008
plotBinOverRegions0.0000.0000.002
preparePool0.0000.0000.001
reCenterPeaks0.0120.0000.013
summarizeOverlapsByBins0.4680.1720.961
summarizePatternInPeaks0.9920.0361.030
tileCount0.5760.1800.917
tileGRanges0.0480.0000.050
toGRanges0.0840.0080.093
translatePattern0.0040.0000.001
wgEncodeTfbsV30.2480.0040.253
write2FASTA0.0280.0000.028
xget0.1520.0000.152