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CHECK report for ChIPpeakAnno on malbec2

This page was generated on 2019-10-16 11:57:33 -0400 (Wed, 16 Oct 2019).

Package 260/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPpeakAnno 3.18.2
Lihua Julie Zhu
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/ChIPpeakAnno
Branch: RELEASE_3_9
Last Commit: 6d1c24d
Last Changed Date: 2019-07-26 13:39:35 -0400 (Fri, 26 Jul 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

Summary

Package: ChIPpeakAnno
Version: 3.18.2
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ChIPpeakAnno_3.18.2.tar.gz
StartedAt: 2019-10-16 00:27:14 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 00:34:40 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 445.7 seconds
RetCode: 0
Status:  OK 
CheckDir: ChIPpeakAnno.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ChIPpeakAnno_3.18.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/ChIPpeakAnno.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘3.18.2’
* 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     12.7Mb
    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 17.457  0.056  17.622
* 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-3.9-bioc/meat/ChIPpeakAnno.Rcheck/00check.log’
for details.



Installation output

ChIPpeakAnno.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL ChIPpeakAnno
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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 version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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, 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
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: 187 | SKIPPED: 5 | WARNINGS: 6 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 67.544   1.168  69.310 

Example timings

ChIPpeakAnno.Rcheck/ChIPpeakAnno-Ex.timings

nameusersystemelapsed
BED2RangedData0.050.000.05
ChIPpeakAnno-package0.0010.0000.000
ExonPlusUtr.human.GRCh374.3950.0604.465
GFF2RangedData0.0120.0040.016
HOT.spots0.1820.0080.190
IDRfilter0.0000.0010.001
Peaks.Ste12.Replicate10.1970.0100.207
Peaks.Ste12.Replicate20.1390.0000.139
Peaks.Ste12.Replicate30.1260.0000.126
TSS.human.GRCh370.1890.0000.190
TSS.human.GRCh380.5510.0120.563
TSS.human.NCBI360.1700.0000.169
TSS.mouse.GRCm380.2380.0040.242
TSS.mouse.NCBIM370.1770.0000.177
TSS.rat.RGSC3.40.1430.0000.143
TSS.rat.Rnor_5.00.1320.0000.131
TSS.zebrafish.Zv80.1280.0040.133
TSS.zebrafish.Zv90.1650.0000.165
addAncestors2.6160.0562.686
addGeneIDs1.8330.0712.008
addMetadata1.1880.0761.263
annoGR0.0000.0000.001
annoPeaks2.2690.1163.437
annotatePeakInBatch2.2680.0562.328
annotatedPeak0.1170.0040.122
assignChromosomeRegion0.0030.0000.002
bdp0.0000.0000.001
binOverFeature0.7780.0000.917
binOverGene0.0020.0000.001
binOverRegions0.0010.0000.002
condenseMatrixByColnames0.0190.0000.019
convert2EntrezID0.3680.0000.373
countPatternInSeqs0.1280.0040.215
cumulativePercentage000
egOrgMap0.0010.0000.000
enrichedGO0.0030.0000.003
estFragmentLength0.0000.0000.001
estLibSize0.0010.0000.000
featureAlignedDistribution0.3340.0120.348
featureAlignedExtentSignal0.0030.0000.003
featureAlignedHeatmap0.4380.0000.439
featureAlignedSignal0.1950.0320.227
findEnhancers17.457 0.05617.622
findOverlappingPeaks0.0000.0020.001
findOverlapsOfPeaks0.4950.0010.497
getAllPeakSequence0.4470.0040.463
getAnnotation000
getEnrichedGO0.0110.0000.011
getEnrichedPATH000
getGeneSeq0.0010.0000.001
getUniqueGOidCount0.0010.0000.001
getVennCounts0.0010.0000.001
hyperGtest0.0010.0000.001
makeVennDiagram0.0020.0000.002
mergePlusMinusPeaks0.0000.0000.001
myPeakList0.0190.0000.019
oligoFrequency0.0030.0040.007
oligoSummary0.0000.0000.001
peakPermTest0.0010.0000.001
peaksNearBDP000
pie10.0080.0000.008
plotBinOverRegions0.0010.0000.000
preparePool000
reCenterPeaks0.0110.0000.012
summarizeOverlapsByBins3.2450.6643.915
summarizePatternInPeaks0.5720.0360.608
tileCount1.1660.2481.563
tileGRanges0.2960.1850.035
toGRanges0.2140.0040.292
translatePattern0.0000.0000.001
wgEncodeTfbsV30.2820.0120.293
write2FASTA0.0090.0040.012
xget0.130.000.13