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This page was generated on 2021-08-02 12:05:08 -0400 (Mon, 02 Aug 2021).

CHECK results for ChIPpeakAnno on merida1

To the developers/maintainers of the ChIPpeakAnno package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ChIPpeakAnno.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 290/2015HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPpeakAnno 3.27.4  (landing page)
Jianhong Ou
Snapshot Date: 2021-08-01 14:50:04 -0400 (Sun, 01 Aug 2021)
URL: https://git.bioconductor.org/packages/ChIPpeakAnno
Branch: master
Last Commit: 18eea1a
Last Changed Date: 2021-07-13 08:15:27 -0400 (Tue, 13 Jul 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ChIPpeakAnno
Version: 3.27.4
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ChIPpeakAnno_3.27.4.tar.gz
StartedAt: 2021-08-02 00:40:59 -0400 (Mon, 02 Aug 2021)
EndedAt: 2021-08-02 00:56:54 -0400 (Mon, 02 Aug 2021)
EllapsedTime: 955.0 seconds
RetCode: 0
Status:   OK  
CheckDir: ChIPpeakAnno.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ChIPpeakAnno_3.27.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/ChIPpeakAnno.Rcheck’
* using R version 4.1.0 RC (2021-05-16 r80304)
* using platform: x86_64-apple-darwin17.0 (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 ‘3.27.4’
* 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 19.6Mb
  sub-directories of 1Mb or more:
    data     13.1Mb
    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 LazyData ... 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            48.031  0.462  48.552
annotatePeakInBatch      22.606  0.574  23.226
findMotifsInPromoterSeqs 22.175  0.189  22.475
annoPeaks                 4.419  0.277  13.287
* 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-3.14-bioc/meat/ChIPpeakAnno.Rcheck/00check.log’
for details.



Installation output

ChIPpeakAnno.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ChIPpeakAnno
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘ChIPpeakAnno’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 4.1.0 RC (2021-05-16 r80304) -- "Camp Pontanezen"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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

Attaching package: 'BiocGenerics'

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.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

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: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

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")
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (5)

[ FAIL 0 | WARN 3 | SKIP 5 | PASS 313 ]
> 
> proc.time()
   user  system elapsed 
355.054   4.281 368.792 

Example timings

ChIPpeakAnno.Rcheck/ChIPpeakAnno-Ex.timings

nameusersystemelapsed
ChIPpeakAnno-package0.0010.0010.001
ExonPlusUtr.human.GRCh373.5430.1193.665
HOT.spots0.1800.0140.194
IDRfilter0.0010.0000.002
Peaks.Ste12.Replicate10.1070.0020.110
Peaks.Ste12.Replicate20.0300.0110.066
Peaks.Ste12.Replicate30.0340.0030.036
TSS.human.GRCh370.2380.0220.261
TSS.human.GRCh380.1790.0160.196
TSS.human.NCBI360.1320.0100.142
TSS.mouse.GRCm380.1220.0120.134
TSS.mouse.NCBIM370.1190.0120.132
TSS.rat.RGSC3.40.0910.0080.098
TSS.rat.Rnor_5.00.0810.0060.087
TSS.zebrafish.Zv80.0740.0070.082
TSS.zebrafish.Zv90.0950.0080.102
addAncestors2.0080.0812.091
addGeneIDs2.5870.5433.134
addMetadata2.7780.1762.959
annoGR0.0000.0000.001
annoPeaks 4.419 0.27713.287
annotatePeakInBatch22.606 0.57423.226
annotatedPeak0.1470.0110.159
assignChromosomeRegion0.0030.0010.003
bdp0.0010.0000.001
binOverFeature1.5660.0171.625
binOverGene0.0010.0010.002
binOverRegions0.0010.0000.001
condenseMatrixByColnames0.0150.0010.016
convert2EntrezID0.4790.0040.483
countPatternInSeqs0.2360.0050.241
cumulativePercentage0.0010.0010.000
downstreams0.0600.0010.061
egOrgMap0.0010.0000.001
enrichedGO0.0030.0020.004
enrichmentPlot0.7550.0170.772
estFragmentLength000
estLibSize0.0010.0000.001
featureAlignedDistribution0.4410.0020.445
featureAlignedExtendSignal0.0030.0010.003
featureAlignedHeatmap0.6510.0030.656
featureAlignedSignal0.4280.0720.501
findEnhancers48.031 0.46248.552
findMotifsInPromoterSeqs22.175 0.18922.475
findOverlappingPeaks0.0020.0010.004
findOverlapsOfPeaks4.0370.0254.110
genomicElementDistribution0.0030.0000.004
genomicElementUpSetR0.0020.0010.003
getAllPeakSequence0.8970.0180.919
getAnnotation0.0020.0010.002
getEnrichedGO0.0150.0080.022
getEnrichedPATH0.0020.0010.002
getGO0.0000.0000.001
getGeneSeq0.0020.0000.003
getUniqueGOidCount0.0010.0000.001
getVennCounts0.0010.0010.001
hyperGtest0.0020.0010.002
makeVennDiagram0.0060.0000.006
mergePlusMinusPeaks0.0010.0000.001
metagenePlot3.2540.0593.319
myPeakList0.0210.0030.023
oligoFrequency0.2130.0140.227
oligoSummary0.0000.0010.001
peakPermTest0.0010.0010.002
peaksNearBDP0.0010.0010.001
pie10.0060.0010.007
plotBinOverRegions0.0010.0010.001
preparePool0.0010.0000.001
reCenterPeaks0.0640.0000.064
summarizeOverlapsByBins3.0720.3233.386
summarizePatternInPeaks1.2970.4831.300
tileCount0.8230.5970.842
tileGRanges0.0870.0130.100
toGRanges0.2590.0300.289
translatePattern0.0000.0000.001
wgEncodeTfbsV30.2740.0140.288
write2FASTA0.0380.0050.043
xget0.1140.0080.123