Back to Multiple platform build/check report for BioC 3.16:   simplified   long
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This page was generated on 2023-04-12 11:06:02 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for ChIPpeakAnno on lconway


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? 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 313/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPpeakAnno 3.32.0  (landing page)
Jianhong Ou
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/ChIPpeakAnno
git_branch: RELEASE_3_16
git_last_commit: 016661f
git_last_commit_date: 2022-11-01 11:04:34 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ChIPpeakAnno
Version: 3.32.0
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_3.32.0.tar.gz
StartedAt: 2023-04-10 19:21:31 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 19:30:49 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 558.2 seconds
RetCode: 0
Status:   OK  
CheckDir: ChIPpeakAnno.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_3.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/ChIPpeakAnno.Rcheck’
* using R version 4.2.3 (2023-03-15)
* 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 ‘3.32.0’
* 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 ... NOTE
oligoFrequency : <anonymous>: no visible global function definition for
  'oligonucleotideFrequency'
Undefined global functions or variables:
  oligonucleotideFrequency
* 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            18.498  0.429  18.992
annotatePeakInBatch      11.811  0.639  12.514
findMotifsInPromoterSeqs 12.008  0.208  12.415
annoPeaks                 2.759  0.281   9.952
* 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-3.16-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/4.2/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 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 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, aperm, 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("reactome.db") || stop("unable to load reactome.db")
Loading required package: reactome.db
[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")
[ FAIL 0 | WARN 4 | SKIP 6 | PASS 316 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (6)

[ FAIL 0 | WARN 4 | SKIP 6 | PASS 316 ]
> 
> proc.time()
   user  system elapsed 
157.565   4.654 170.065 

Example timings

ChIPpeakAnno.Rcheck/ChIPpeakAnno-Ex.timings

nameusersystemelapsed
ChIPpeakAnno-package000
ExonPlusUtr.human.GRCh373.0360.0843.127
HOT.spots0.1090.0070.117
IDRfilter0.0010.0000.001
Peaks.Ste12.Replicate10.0380.0030.040
Peaks.Ste12.Replicate20.0090.0020.010
Peaks.Ste12.Replicate30.0090.0020.010
TSS.human.GRCh370.1490.0080.156
TSS.human.GRCh380.1210.0070.128
TSS.human.NCBI360.1080.0050.113
TSS.mouse.GRCm380.1010.0080.109
TSS.mouse.NCBIM370.0940.0080.102
TSS.rat.RGSC3.40.0770.0070.083
TSS.rat.Rnor_5.00.0650.0050.070
TSS.zebrafish.Zv80.0660.0070.072
TSS.zebrafish.Zv90.0860.0080.095
addAncestors1.1900.0581.256
addGeneIDs1.9770.6832.683
addMetadata1.3850.0691.458
annoGR0.0010.0000.001
annoPeaks2.7590.2819.952
annotatePeakInBatch11.811 0.63912.514
annotatedPeak0.0450.0060.051
assignChromosomeRegion0.0020.0010.003
bdp0.0000.0000.001
binOverFeature0.6680.0180.690
binOverGene0.0010.0000.002
binOverRegions0.0010.0010.002
condenseMatrixByColnames0.0080.0010.009
convert2EntrezID0.3720.0050.380
countPatternInSeqs0.1480.0050.154
cumulativePercentage000
downstreams0.0220.0000.023
egOrgMap0.0000.0010.001
enrichedGO0.0020.0020.004
enrichmentPlot0.5790.0200.602
estFragmentLength0.0000.0000.001
estLibSize0.0000.0000.001
featureAlignedDistribution0.1880.0020.191
featureAlignedExtendSignal0.0020.0010.002
featureAlignedHeatmap0.2860.0030.292
featureAlignedSignal0.1730.0970.272
findEnhancers18.498 0.42918.992
findMotifsInPromoterSeqs12.008 0.20812.415
findOverlappingPeaks0.0010.0000.001
findOverlapsOfPeaks1.5540.0191.579
genomicElementDistribution0.0010.0000.002
genomicElementUpSetR0.0000.0010.001
getAllPeakSequence0.4420.0180.466
getAnnotation0.0010.0010.002
getEnrichedGO0.0090.0050.014
getEnrichedPATH000
getGO0.0000.0000.001
getGeneSeq0.0010.0010.002
getUniqueGOidCount0.0000.0000.001
getVennCounts0.0010.0000.001
hyperGtest0.0010.0010.001
makeVennDiagram0.0020.0000.003
mergePlusMinusPeaks0.0000.0000.001
metagenePlot1.9350.0472.001
myPeakList0.0140.0020.015
oligoFrequency0.1870.0120.201
oligoSummary0.0000.0010.001
peakPermTest0.0010.0000.002
peaksNearBDP0.0010.0000.001
pie10.0040.0000.005
plotBinOverRegions0.0010.0000.000
preparePool0.0000.0000.001
reCenterPeaks0.0220.0000.023
summarizeOverlapsByBins2.8760.5803.053
summarizePatternInPeaks0.4610.0410.515
tileCount0.4990.4570.541
tileGRanges0.0320.0200.053
toGRanges0.1050.0230.129
translatePattern0.0010.0010.000
wgEncodeTfbsV30.2040.0120.217
write2FASTA0.0130.0050.017
xget0.0890.0090.101