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This page was generated on 2021-09-17 15:06:32 -0400 (Fri, 17 Sep 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.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 294/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPpeakAnno 3.26.4  (landing page)
Jianhong Ou
Snapshot Date: 2021-09-16 04:50:11 -0400 (Thu, 16 Sep 2021)
git_url: https://git.bioconductor.org/packages/ChIPpeakAnno
git_branch: RELEASE_3_13
git_last_commit: 5104b7d
git_last_commit_date: 2021-09-09 15:41:30 -0400 (Thu, 09 Sep 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: 3.26.4
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_3.26.4.tar.gz
StartedAt: 2021-09-16 17:22:47 -0400 (Thu, 16 Sep 2021)
EndedAt: 2021-09-16 17:35:04 -0400 (Thu, 16 Sep 2021)
EllapsedTime: 736.5 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_3.26.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/ChIPpeakAnno.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘3.26.4’
* 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            43.961  0.440  44.434
annotatePeakInBatch      20.183  0.532  20.771
findMotifsInPromoterSeqs 20.402  0.143  20.668
annoPeaks                 4.630  0.288   7.192
* 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 4.1.1 (2021-08-10) -- "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
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 (6)

[ FAIL 0 | WARN 3 | SKIP 6 | PASS 214 ]
> 
> proc.time()
   user  system elapsed 
179.595   3.714 187.988 

Example timings

ChIPpeakAnno.Rcheck/ChIPpeakAnno-Ex.timings

nameusersystemelapsed
ChIPpeakAnno-package0.0010.0000.001
ExonPlusUtr.human.GRCh373.3990.1053.507
HOT.spots0.2000.0100.211
IDRfilter0.0010.0000.002
Peaks.Ste12.Replicate10.1110.0030.114
Peaks.Ste12.Replicate20.0360.0050.041
Peaks.Ste12.Replicate30.0360.0030.039
TSS.human.GRCh370.2480.0210.268
TSS.human.GRCh380.1550.0100.166
TSS.human.NCBI360.1250.0080.134
TSS.mouse.GRCm380.1250.0140.140
TSS.mouse.NCBIM370.1240.0120.138
TSS.rat.RGSC3.40.1100.0060.117
TSS.rat.Rnor_5.00.0700.0060.074
TSS.zebrafish.Zv80.0820.0060.087
TSS.zebrafish.Zv90.0990.0070.106
addAncestors1.5340.0591.595
addGeneIDs2.4910.5223.014
addMetadata2.8380.1833.022
annoGR000
annoPeaks4.6300.2887.192
annotatePeakInBatch20.183 0.53220.771
annotatedPeak0.0740.0040.079
assignChromosomeRegion0.0010.0010.003
bdp0.0010.0010.001
binOverFeature1.5790.0171.600
binOverGene0.0020.0010.002
binOverRegions0.0010.0010.002
condenseMatrixByColnames0.0210.0010.022
convert2EntrezID0.6150.0110.626
countPatternInSeqs0.2540.0060.260
cumulativePercentage000
downstreams0.0460.0000.047
egOrgMap000
enrichedGO0.0020.0020.004
enrichmentPlot0.6250.0090.635
estFragmentLength0.0010.0000.000
estLibSize0.0010.0000.001
featureAlignedDistribution0.4830.0020.485
featureAlignedExtendSignal0.0030.0010.003
featureAlignedHeatmap0.6060.0030.610
featureAlignedSignal0.5500.0550.606
findEnhancers43.961 0.44044.434
findMotifsInPromoterSeqs20.402 0.14320.668
findOverlappingPeaks0.0020.0010.003
findOverlapsOfPeaks4.8640.0394.908
genomicElementDistribution0.0030.0010.005
genomicElementUpSetR0.0010.0000.002
getAllPeakSequence1.0020.0231.027
getAnnotation0.0030.0020.004
getEnrichedGO0.0180.0080.027
getEnrichedPATH0.0010.0010.002
getGO0.0010.0000.001
getGeneSeq0.0020.0010.004
getUniqueGOidCount0.0010.0000.001
getVennCounts0.0020.0010.002
hyperGtest0.0020.0010.002
makeVennDiagram0.0060.0010.006
mergePlusMinusPeaks0.0010.0010.002
metagenePlot3.4260.0493.479
myPeakList0.0180.0030.021
oligoFrequency0.2900.0150.305
oligoSummary0.0010.0010.002
peakPermTest0.0020.0010.003
peaksNearBDP0.0010.0000.002
pie10.0080.0010.009
plotBinOverRegions0.0010.0010.001
preparePool0.0010.0000.001
reCenterPeaks0.0660.0000.066
summarizeOverlapsByBins3.7530.6493.809
summarizePatternInPeaks1.1080.0911.199
tileCount0.8920.5930.918
tileGRanges0.1050.0140.119
toGRanges0.2940.0380.333
translatePattern0.0010.0010.002
wgEncodeTfbsV30.3310.0170.348
write2FASTA0.0450.0040.049
xget0.1710.0100.181