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This page was generated on 2021-10-22 12:04:53 -0400 (Fri, 22 Oct 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.
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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: /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_3.27.7.tar.gz
StartedAt: 2021-10-22 01:52:20 -0400 (Fri, 22 Oct 2021)
EndedAt: 2021-10-22 02:09:09 -0400 (Fri, 22 Oct 2021)
EllapsedTime: 1008.4 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_3.27.7.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/ChIPpeakAnno.Rcheck’
* using R version 4.1.1 Patched (2021-08-22 r80813)
* 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 ‘3.27.7’
* 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            45.299  0.428  45.799
annotatePeakInBatch      24.157  0.579  24.789
findMotifsInPromoterSeqs 20.068  0.209  20.399
annoPeaks                 4.874  0.273  12.444
* 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 4.1.1 Patched (2021-08-22 r80813) -- "Kick Things"
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 (6)

[ FAIL 0 | WARN 3 | SKIP 6 | PASS 313 ]
> 
> proc.time()
   user  system elapsed 
365.744   4.505 373.268 

Example timings

ChIPpeakAnno.Rcheck/ChIPpeakAnno-Ex.timings

nameusersystemelapsed
ChIPpeakAnno-package0.0010.0000.000
ExonPlusUtr.human.GRCh374.7580.1414.905
HOT.spots0.2020.0140.216
IDRfilter0.0010.0010.002
Peaks.Ste12.Replicate10.0910.0030.095
Peaks.Ste12.Replicate20.0320.0020.034
Peaks.Ste12.Replicate30.0320.0030.036
TSS.human.GRCh370.2520.0200.271
TSS.human.GRCh380.1940.0160.210
TSS.human.NCBI360.1430.0110.155
TSS.mouse.GRCm380.1360.0120.148
TSS.mouse.NCBIM370.1260.0110.137
TSS.rat.RGSC3.40.1170.0100.128
TSS.rat.Rnor_5.00.0860.0090.096
TSS.zebrafish.Zv80.0940.0090.102
TSS.zebrafish.Zv90.1140.0090.124
addAncestors2.1510.0832.237
addGeneIDs3.0270.5973.629
addMetadata3.0040.2213.229
annoGR000
annoPeaks 4.874 0.27312.444
annotatePeakInBatch24.157 0.57924.789
annotatedPeak0.0820.0040.086
assignChromosomeRegion0.0020.0000.003
bdp0.0010.0000.001
binOverFeature1.7530.0251.782
binOverGene0.0010.0000.002
binOverRegions0.0010.0000.002
condenseMatrixByColnames0.0210.0000.021
convert2EntrezID0.4970.0040.502
countPatternInSeqs0.2320.0050.238
cumulativePercentage000
downstreams0.0670.0000.068
egOrgMap0.0010.0000.001
enrichedGO0.0030.0030.006
enrichmentPlot0.7180.0100.730
estFragmentLength0.0010.0000.001
estLibSize0.0010.0000.001
featureAlignedDistribution0.4730.0020.476
featureAlignedExtendSignal0.0030.0000.003
featureAlignedHeatmap0.8220.0080.832
featureAlignedSignal0.4330.0370.472
findEnhancers45.299 0.42845.799
findMotifsInPromoterSeqs20.068 0.20920.399
findOverlappingPeaks0.0020.0010.002
findOverlapsOfPeaks4.5850.0364.628
genomicElementDistribution0.0020.0010.003
genomicElementUpSetR0.0010.0000.002
getAllPeakSequence0.9520.0170.973
getAnnotation0.0020.0000.003
getEnrichedGO0.0140.0030.017
getEnrichedPATH0.0010.0000.002
getGO0.0010.0000.001
getGeneSeq0.0030.0000.003
getUniqueGOidCount0.0010.0010.001
getVennCounts0.0010.0000.001
hyperGtest0.0020.0000.002
makeVennDiagram0.0050.0010.005
mergePlusMinusPeaks0.0010.0000.001
metagenePlot3.7040.0553.771
myPeakList0.0210.0030.024
oligoFrequency0.2680.0120.281
oligoSummary0.0000.0000.001
peakPermTest0.0020.0010.002
peaksNearBDP0.0010.0000.002
pie10.0070.0000.007
plotBinOverRegions0.0010.0000.001
preparePool0.0010.0000.001
reCenterPeaks0.0810.0000.082
summarizeOverlapsByBins3.7700.7173.875
summarizePatternInPeaks1.0490.0881.138
tileCount0.8880.6210.905
tileGRanges0.0890.0160.106
toGRanges0.2500.0290.279
translatePattern0.0010.0010.001
wgEncodeTfbsV30.3090.0180.326
write2FASTA0.0410.0040.045
xget0.1490.0100.159