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This page was generated on 2021-10-22 12:03:56 -0400 (Fri, 22 Oct 2021).

CHECK results for ChIPpeakAnno on nebbiolo2

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 299/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPpeakAnno 3.27.7  (landing page)
Jianhong Ou
Snapshot Date: 2021-10-21 14:50:08 -0400 (Thu, 21 Oct 2021)
git_url: https://git.bioconductor.org/packages/ChIPpeakAnno
git_branch: master
git_last_commit: 3c2c9fb
git_last_commit_date: 2021-10-19 09:12:15 -0400 (Tue, 19 Oct 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: 3.27.7
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings ChIPpeakAnno_3.27.7.tar.gz
StartedAt: 2021-10-21 19:29:08 -0400 (Thu, 21 Oct 2021)
EndedAt: 2021-10-21 19:39:10 -0400 (Thu, 21 Oct 2021)
EllapsedTime: 601.3 seconds
RetCode: 0
Status:   OK  
CheckDir: ChIPpeakAnno.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings ChIPpeakAnno_3.27.7.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/ChIPpeakAnno.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘3.27.7’
* 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 19.1Mb
  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 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            24.757  0.444  25.201
annotatePeakInBatch      12.063  0.296  12.373
findMotifsInPromoterSeqs 11.657  0.192  11.864
* 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
  ‘/home/biocbuild/bbs-3.14-bioc/meat/ChIPpeakAnno.Rcheck/00check.log’
for details.



Installation output

ChIPpeakAnno.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL ChIPpeakAnno
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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: 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 (6)

[ FAIL 0 | WARN 3 | SKIP 6 | PASS 313 ]
> 
> proc.time()
   user  system elapsed 
203.930   4.783 211.134 

Example timings

ChIPpeakAnno.Rcheck/ChIPpeakAnno-Ex.timings

nameusersystemelapsed
ChIPpeakAnno-package000
ExonPlusUtr.human.GRCh373.4840.1763.659
HOT.spots0.1340.0040.138
IDRfilter0.0010.0000.000
Peaks.Ste12.Replicate10.0550.0000.055
Peaks.Ste12.Replicate20.0120.0040.016
Peaks.Ste12.Replicate30.0170.0000.016
TSS.human.GRCh370.1910.0110.203
TSS.human.GRCh380.1510.0080.158
TSS.human.NCBI360.1220.0280.150
TSS.mouse.GRCm380.100.020.12
TSS.mouse.NCBIM370.0900.0120.102
TSS.rat.RGSC3.40.0820.0040.086
TSS.rat.Rnor_5.00.0730.0000.074
TSS.zebrafish.Zv80.0600.0160.077
TSS.zebrafish.Zv90.0870.0080.095
addAncestors1.1650.0281.192
addGeneIDs1.7830.0881.873
addMetadata1.5790.1481.727
annoGR000
annoPeaks3.8310.1924.770
annotatePeakInBatch12.063 0.29612.373
annotatedPeak0.0690.0000.069
assignChromosomeRegion0.0000.0000.001
bdp000
binOverFeature1.3230.0321.356
binOverGene0.0000.0000.001
binOverRegions0.0010.0000.000
condenseMatrixByColnames0.0160.0000.016
convert2EntrezID0.50.00.5
countPatternInSeqs0.1580.0000.158
cumulativePercentage0.0010.0000.000
downstreams0.0390.0000.039
egOrgMap0.0010.0000.001
enrichedGO0.0010.0030.002
enrichmentPlot0.4190.0010.421
estFragmentLength000
estLibSize000
featureAlignedDistribution0.3070.0160.323
featureAlignedExtendSignal0.0010.0000.001
featureAlignedHeatmap0.4350.0000.435
featureAlignedSignal0.320.000.32
findEnhancers24.757 0.44425.201
findMotifsInPromoterSeqs11.657 0.19211.864
findOverlappingPeaks0.0010.0000.000
findOverlapsOfPeaks2.4320.0282.461
genomicElementDistribution0.0010.0000.000
genomicElementUpSetR000
getAllPeakSequence0.7100.0280.738
getAnnotation0.0010.0000.000
getEnrichedGO0.0080.0000.009
getEnrichedPATH0.0000.0000.001
getGO000
getGeneSeq0.0010.0000.000
getUniqueGOidCount0.0010.0000.001
getVennCounts0.0000.0000.001
hyperGtest0.0010.0000.001
makeVennDiagram0.0020.0000.001
mergePlusMinusPeaks0.0010.0000.000
metagenePlot2.1440.0192.164
myPeakList0.0140.0000.014
oligoFrequency0.150.000.15
oligoSummary0.0010.0000.001
peakPermTest0.0010.0000.001
peaksNearBDP000
pie10.0050.0000.005
plotBinOverRegions0.0010.0000.001
preparePool000
reCenterPeaks0.0380.0000.038
summarizeOverlapsByBins3.3740.3563.391
summarizePatternInPeaks0.6890.0320.721
tileCount0.5400.3260.485
tileGRanges0.0710.0040.075
toGRanges0.1530.0160.169
translatePattern000
wgEncodeTfbsV30.2340.0040.238
write2FASTA0.0230.0000.023
xget0.1040.0080.112