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This page was generated on 2021-08-02 15:05:37 -0400 (Mon, 02 Aug 2021).

CHECK results for ChIPpeakAnno on machv2

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 294/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPpeakAnno 3.26.2  (landing page)
Jianhong Ou
Snapshot Date: 2021-08-01 04:50:10 -0400 (Sun, 01 Aug 2021)
URL: https://git.bioconductor.org/packages/ChIPpeakAnno
Branch: RELEASE_3_13
Last Commit: da90a6c
Last Changed Date: 2021-07-13 11:27:12 -0400 (Tue, 13 Jul 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ChIPpeakAnno
Version: 3.26.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ChIPpeakAnno_3.26.2.tar.gz
StartedAt: 2021-08-01 16:51:49 -0400 (Sun, 01 Aug 2021)
EndedAt: 2021-08-01 17:04:01 -0400 (Sun, 01 Aug 2021)
EllapsedTime: 731.5 seconds
RetCode: 0
Status:   OK  
CheckDir: ChIPpeakAnno.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ChIPpeakAnno_3.26.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/ChIPpeakAnno.Rcheck’
* using R version 4.1.0 (2021-05-18)
* 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 ‘3.26.2’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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            42.416  0.408  42.861
annotatePeakInBatch      21.382  0.505  21.900
findMotifsInPromoterSeqs 19.233  0.163  19.507
annoPeaks                 4.145  0.254   6.566
* 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-3.13-bioc/meat/ChIPpeakAnno.Rcheck/00check.log’
for details.



Installation output

ChIPpeakAnno.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/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 (2021-05-18) -- "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
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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 1 | SKIP 5 | PASS 214 ]
> 
> proc.time()
   user  system elapsed 
178.408   3.787 185.407 

Example timings

ChIPpeakAnno.Rcheck/ChIPpeakAnno-Ex.timings

nameusersystemelapsed
ChIPpeakAnno-package0.0010.0010.000
ExonPlusUtr.human.GRCh373.3090.1043.415
HOT.spots0.1430.0080.151
IDRfilter0.0010.0010.001
Peaks.Ste12.Replicate10.0770.0020.080
Peaks.Ste12.Replicate20.0270.0020.029
Peaks.Ste12.Replicate30.0290.0030.031
TSS.human.GRCh370.1910.0150.207
TSS.human.GRCh380.1430.0070.149
TSS.human.NCBI360.1060.0060.111
TSS.mouse.GRCm380.0990.0070.106
TSS.mouse.NCBIM370.1180.0060.124
TSS.rat.RGSC3.40.1010.0100.112
TSS.rat.Rnor_5.00.0760.0060.083
TSS.zebrafish.Zv80.0780.0060.085
TSS.zebrafish.Zv90.1090.0060.116
addAncestors1.7290.0781.810
addGeneIDs2.6560.5383.196
addMetadata2.8000.0592.861
annoGR0.0000.0000.001
annoPeaks4.1450.2546.566
annotatePeakInBatch21.382 0.50521.900
annotatedPeak0.0760.0040.080
assignChromosomeRegion0.0030.0010.004
bdp0.0000.0000.001
binOverFeature2.7310.0542.788
binOverGene0.0010.0000.002
binOverRegions0.0010.0000.001
condenseMatrixByColnames0.0190.0010.020
convert2EntrezID0.4480.0040.453
countPatternInSeqs0.2190.0050.225
cumulativePercentage0.0000.0000.001
downstreams0.0540.0010.055
egOrgMap0.0000.0000.001
enrichedGO0.0030.0020.006
enrichmentPlot0.5290.0080.537
estFragmentLength0.0010.0010.001
estLibSize0.0000.0000.001
featureAlignedDistribution0.5120.0340.546
featureAlignedExtendSignal0.0020.0000.002
featureAlignedHeatmap0.7180.0530.771
featureAlignedSignal0.3900.1280.517
findEnhancers42.416 0.40842.861
findMotifsInPromoterSeqs19.233 0.16319.507
findOverlappingPeaks0.0020.0010.003
findOverlapsOfPeaks4.8340.0484.889
genomicElementDistribution0.0040.0010.005
genomicElementUpSetR0.0010.0000.003
getAllPeakSequence0.9110.0160.930
getAnnotation0.0030.0010.004
getEnrichedGO0.0180.0080.026
getEnrichedPATH0.0020.0010.003
getGO0.0000.0000.001
getGeneSeq0.0030.0010.004
getUniqueGOidCount0.0010.0000.001
getVennCounts0.0010.0010.002
hyperGtest0.0010.0010.001
makeVennDiagram0.0030.0010.004
mergePlusMinusPeaks0.0000.0010.001
metagenePlot3.6900.0553.754
myPeakList0.0200.0030.023
oligoFrequency0.3010.0140.315
oligoSummary0.0000.0000.001
peakPermTest0.0010.0000.002
peaksNearBDP0.0020.0000.001
pie10.0080.0010.010
plotBinOverRegions0.0010.0000.002
preparePool0.0010.0000.001
reCenterPeaks0.0950.0000.096
summarizeOverlapsByBins3.4550.5953.525
summarizePatternInPeaks1.0760.0941.171
tileCount0.8980.5850.893
tileGRanges0.0970.0150.112
toGRanges0.2920.0370.329
translatePattern0.0010.0000.001
wgEncodeTfbsV30.2760.0110.288
write2FASTA0.0340.0040.039
xget0.1140.0070.122