Back to Multiple platform build/check report for BioC 3.16
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This page was generated on 2022-08-11 11:07:54 -0400 (Thu, 11 Aug 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4375
palomino4Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4159
lconwaymacOS 12.2.1 Montereyx86_644.2.1 Patched (2022-07-09 r82577) -- "Funny-Looking Kid" 4165
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 307/2139HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPpeakAnno 3.31.2  (landing page)
Jianhong Ou
Snapshot Date: 2022-08-10 14:00:02 -0400 (Wed, 10 Aug 2022)
git_url: https://git.bioconductor.org/packages/ChIPpeakAnno
git_branch: master
git_last_commit: 75bb5e2
git_last_commit_date: 2022-08-10 09:11:21 -0400 (Wed, 10 Aug 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  YES
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  YES
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    OK    OK  YES

Summary

Package: ChIPpeakAnno
Version: 3.31.2
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_3.31.2.tar.gz
StartedAt: 2022-08-10 19:25:51 -0400 (Wed, 10 Aug 2022)
EndedAt: 2022-08-10 19:35:36 -0400 (Wed, 10 Aug 2022)
EllapsedTime: 584.8 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_3.31.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/ChIPpeakAnno.Rcheck’
* using R version 4.2.1 Patched (2022-07-09 r82577)
* 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 ‘3.31.2’
* 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            22.393  0.453  22.944
annotatePeakInBatch      13.130  0.603  13.804
findMotifsInPromoterSeqs 13.226  0.232  13.639
annoPeaks                 2.821  0.267  10.263
* 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-3.16-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 4.2.1 Patched (2022-07-09 r82577) -- "Funny-Looking Kid"
Copyright (C) 2022 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("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 3 | SKIP 6 | PASS 316 ]

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

[ FAIL 0 | WARN 3 | SKIP 6 | PASS 316 ]
> 
> proc.time()
   user  system elapsed 
168.385   4.708 176.036 

Example timings

ChIPpeakAnno.Rcheck/ChIPpeakAnno-Ex.timings

nameusersystemelapsed
ChIPpeakAnno-package0.0010.0000.001
ExonPlusUtr.human.GRCh373.1060.0903.206
HOT.spots0.1290.0110.141
IDRfilter0.0010.0000.001
Peaks.Ste12.Replicate10.0420.0030.045
Peaks.Ste12.Replicate20.0150.0020.017
Peaks.Ste12.Replicate30.0130.0020.015
TSS.human.GRCh370.1890.0110.201
TSS.human.GRCh380.1460.0090.156
TSS.human.NCBI360.0960.0030.099
TSS.mouse.GRCm380.1030.0100.112
TSS.mouse.NCBIM370.0880.0070.097
TSS.rat.RGSC3.40.0770.0060.084
TSS.rat.Rnor_5.00.0710.0060.078
TSS.zebrafish.Zv80.0790.0050.083
TSS.zebrafish.Zv90.0830.0070.091
addAncestors1.2940.0681.375
addGeneIDs2.0370.7052.765
addMetadata1.3670.1001.474
annoGR0.0010.0010.001
annoPeaks 2.821 0.26710.263
annotatePeakInBatch13.130 0.60313.804
annotatedPeak0.0570.0040.062
assignChromosomeRegion0.0010.0010.002
bdp000
binOverFeature0.8560.0310.893
binOverGene0.0010.0000.001
binOverRegions0.0000.0000.001
condenseMatrixByColnames0.0100.0010.010
convert2EntrezID0.4250.0060.432
countPatternInSeqs0.1890.0060.196
cumulativePercentage0.0000.0000.001
downstreams0.0270.0000.028
egOrgMap000
enrichedGO0.0010.0020.003
enrichmentPlot0.4640.0100.476
estFragmentLength0.0000.0000.001
estLibSize000
featureAlignedDistribution0.2430.0040.249
featureAlignedExtendSignal0.0010.0000.002
featureAlignedHeatmap0.3630.0040.369
featureAlignedSignal0.2800.0440.325
findEnhancers22.393 0.45322.944
findMotifsInPromoterSeqs13.226 0.23213.639
findOverlappingPeaks0.0010.0010.002
findOverlapsOfPeaks1.7960.0371.840
genomicElementDistribution0.0020.0010.002
genomicElementUpSetR0.0010.0010.001
getAllPeakSequence0.4970.0180.520
getAnnotation0.0010.0010.002
getEnrichedGO0.0090.0050.014
getEnrichedPATH0.0010.0010.001
getGO000
getGeneSeq0.0020.0000.003
getUniqueGOidCount0.0010.0000.001
getVennCounts0.0010.0000.001
hyperGtest0.0010.0000.001
makeVennDiagram0.0020.0000.002
mergePlusMinusPeaks0.0010.0000.001
metagenePlot2.1690.0762.256
myPeakList0.0130.0020.015
oligoFrequency0.1800.0140.194
oligoSummary0.0000.0000.001
peakPermTest0.0020.0000.002
peaksNearBDP0.0000.0000.001
pie10.0040.0010.005
plotBinOverRegions0.0010.0010.001
preparePool0.0010.0000.000
reCenterPeaks0.0300.0010.030
summarizeOverlapsByBins2.8150.5752.974
summarizePatternInPeaks0.5480.0520.601
tileCount0.5300.5040.605
tileGRanges0.0320.0070.038
toGRanges0.1120.0150.129
translatePattern000
wgEncodeTfbsV30.2080.0120.221
write2FASTA0.0170.0030.019
xget0.1060.0130.120