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CHECK report for ChIPpeakAnno on merida2

This page was generated on 2019-04-09 13:24:52 -0400 (Tue, 09 Apr 2019).

Package 255/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPpeakAnno 3.17.2
Lihua Julie Zhu
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/ChIPpeakAnno
Branch: master
Last Commit: ea2215b
Last Changed Date: 2019-01-22 13:02:27 -0400 (Tue, 22 Jan 2019)
malbec2 Linux (Ubuntu 18.04.2 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK 

Summary

Package: ChIPpeakAnno
Version: 3.17.2
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_3.17.2.tar.gz
StartedAt: 2019-04-08 23:49:56 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 23:57:42 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 465.7 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_3.17.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/ChIPpeakAnno.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘3.17.2’
* 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 17.84  0.181  18.211
* 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-3.9-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/3.6/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 Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 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, 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: 193 SKIPPED: 5 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 77.291   2.510  80.761 

Example timings

ChIPpeakAnno.Rcheck/ChIPpeakAnno-Ex.timings

nameusersystemelapsed
BED2RangedData0.0510.0000.051
ChIPpeakAnno-package0.0010.0000.001
ExonPlusUtr.human.GRCh373.7270.1263.880
GFF2RangedData0.0150.0000.016
HOT.spots0.1740.0390.214
IDRfilter0.0010.0000.002
Peaks.Ste12.Replicate10.3290.0060.337
Peaks.Ste12.Replicate20.1690.0040.173
Peaks.Ste12.Replicate30.1480.0210.173
TSS.human.GRCh370.2020.0350.241
TSS.human.GRCh380.6460.0130.665
TSS.human.NCBI360.1960.0410.237
TSS.mouse.GRCm380.1740.0400.218
TSS.mouse.NCBIM370.1540.0390.196
TSS.rat.RGSC3.40.2180.0420.262
TSS.rat.Rnor_5.00.1090.0340.142
TSS.zebrafish.Zv80.1260.0360.165
TSS.zebrafish.Zv90.1560.0360.194
addAncestors2.9070.1293.076
addGeneIDs1.8530.2412.125
addMetadata1.2720.0771.359
annoGR0.0010.0000.001
annoPeaks2.3140.2592.624
annotatePeakInBatch2.5590.1792.759
annotatedPeak0.1280.0040.134
assignChromosomeRegion0.0050.0000.005
bdp0.0010.0000.001
binOverFeature0.9000.0260.947
binOverGene0.0020.0000.002
binOverRegions0.0030.0010.003
condenseMatrixByColnames0.0180.0000.019
convert2EntrezID0.3460.0060.354
countPatternInSeqs0.1390.0000.142
cumulativePercentage0.0010.0000.000
egOrgMap0.0000.0000.001
enrichedGO0.0040.0020.006
estFragmentLength0.0010.0000.001
estLibSize0.0020.0000.002
featureAlignedDistribution0.2430.0010.251
featureAlignedExtentSignal0.0030.0010.003
featureAlignedHeatmap0.4610.0040.470
featureAlignedSignal0.1930.0410.236
findEnhancers17.840 0.18118.211
findOverlappingPeaks0.0030.0010.004
findOverlapsOfPeaks0.6160.0050.635
getAllPeakSequence0.5720.0230.608
getAnnotation0.0010.0000.001
getEnrichedGO0.0210.0020.023
getEnrichedPATH0.0010.0000.002
getGeneSeq0.0050.0010.006
getUniqueGOidCount0.0020.0000.001
getVennCounts0.0030.0010.003
hyperGtest0.0020.0000.002
makeVennDiagram0.0050.0000.004
mergePlusMinusPeaks0.0020.0000.002
myPeakList0.0180.0020.020
oligoFrequency0.0070.0010.010
oligoSummary0.0010.0000.000
peakPermTest0.0010.0000.002
peaksNearBDP0.0010.0000.001
pie10.0100.0000.011
plotBinOverRegions0.0030.0010.003
preparePool0.0020.0000.001
reCenterPeaks0.0210.0010.021
summarizeOverlapsByBins0.8760.6111.007
summarizePatternInPeaks0.6330.0700.706
tileCount0.5680.3520.545
tileGRanges0.0450.0230.068
toGRanges0.3380.0680.410
translatePattern0.0010.0010.001
wgEncodeTfbsV30.2550.0160.271
write2FASTA0.0180.0020.020
xget0.1020.0070.110