Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-01-26 11:05:46 -0500 (Wed, 26 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4164
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4059
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4001
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4118
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 nebbiolo1


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 299/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPpeakAnno 3.29.3  (landing page)
Jianhong Ou
Snapshot Date: 2022-01-25 13:55:17 -0500 (Tue, 25 Jan 2022)
git_url: https://git.bioconductor.org/packages/ChIPpeakAnno
git_branch: master
git_last_commit: a414709
git_last_commit_date: 2022-01-06 13:23:08 -0500 (Thu, 06 Jan 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'IRanges' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ChIPpeakAnno
Version: 3.29.3
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings ChIPpeakAnno_3.29.3.tar.gz
StartedAt: 2022-01-25 18:32:52 -0500 (Tue, 25 Jan 2022)
EndedAt: 2022-01-25 18:41:26 -0500 (Tue, 25 Jan 2022)
EllapsedTime: 514.1 seconds
RetCode: 0
Status:   OK  
CheckDir: ChIPpeakAnno.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings ChIPpeakAnno_3.29.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/ChIPpeakAnno.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-pc-linux-gnu (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 ‘3.29.3’
* 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 17.5Mb
  sub-directories of 1Mb or more:
    data     12.7Mb
    extdata   3.6Mb
* 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            19.216  0.364  19.582
findMotifsInPromoterSeqs 12.537  0.228  12.766
annotatePeakInBatch      10.947  0.436  11.397
* 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
  ‘/home/biocbuild/bbs-3.15-bioc/meat/ChIPpeakAnno.Rcheck/00check.log’
for details.



Installation output

ChIPpeakAnno.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL ChIPpeakAnno
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/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 Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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")
[ FAIL 0 | WARN 3 | SKIP 6 | PASS 313 ]

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

[ FAIL 0 | WARN 3 | SKIP 6 | PASS 313 ]
> 
> proc.time()
   user  system elapsed 
144.571   5.393 151.836 

Example timings

ChIPpeakAnno.Rcheck/ChIPpeakAnno-Ex.timings

nameusersystemelapsed
ChIPpeakAnno-package0.0000.0000.001
ExonPlusUtr.human.GRCh373.5250.1353.661
HOT.spots0.1310.0130.142
IDRfilter0.0010.0000.001
Peaks.Ste12.Replicate10.0470.0000.048
Peaks.Ste12.Replicate20.0110.0000.012
Peaks.Ste12.Replicate30.0120.0000.011
TSS.human.GRCh370.1910.0030.194
TSS.human.GRCh380.1480.0010.148
TSS.human.NCBI360.1080.0160.123
TSS.mouse.GRCm380.0920.0150.109
TSS.mouse.NCBIM370.0920.0080.099
TSS.rat.RGSC3.40.0850.0010.086
TSS.rat.Rnor_5.00.0740.0000.075
TSS.zebrafish.Zv80.0680.0080.075
TSS.zebrafish.Zv90.0830.0070.091
addAncestors1.1720.0481.219
addGeneIDs1.6520.1871.841
addMetadata0.9340.1601.093
annoGR000
annoPeaks2.7870.3263.868
annotatePeakInBatch10.947 0.43611.397
annotatedPeak0.0450.0080.054
assignChromosomeRegion0.0010.0000.001
bdp0.0000.0000.001
binOverFeature0.6970.0160.714
binOverGene0.0010.0000.000
binOverRegions0.0010.0000.001
condenseMatrixByColnames0.0090.0000.010
convert2EntrezID0.2970.0040.301
countPatternInSeqs0.1350.0040.139
cumulativePercentage000
downstreams0.0130.0070.020
egOrgMap0.0010.0000.000
enrichedGO0.0020.0000.002
enrichmentPlot0.3830.0000.383
estFragmentLength0.0000.0000.001
estLibSize000
featureAlignedDistribution0.2000.0160.216
featureAlignedExtendSignal0.0000.0010.001
featureAlignedHeatmap0.3540.0060.360
featureAlignedSignal0.1720.0600.231
findEnhancers19.216 0.36419.582
findMotifsInPromoterSeqs12.537 0.22812.766
findOverlappingPeaks0.0010.0000.002
findOverlapsOfPeaks1.6520.0041.656
genomicElementDistribution0.0010.0000.001
genomicElementUpSetR000
getAllPeakSequence0.4690.0000.470
getAnnotation0.0010.0000.001
getEnrichedGO0.0110.0000.011
getEnrichedPATH0.0000.0000.001
getGO000
getGeneSeq0.0000.0010.001
getUniqueGOidCount0.0000.0010.001
getVennCounts0.0000.0020.001
hyperGtest0.0000.0020.001
makeVennDiagram0.0000.0020.002
mergePlusMinusPeaks0.0000.0010.000
metagenePlot1.9670.0201.990
myPeakList0.0160.0000.016
oligoFrequency0.1570.0000.157
oligoSummary0.0010.0000.001
peakPermTest0.0000.0010.002
peaksNearBDP0.0000.0000.001
pie10.0050.0000.005
plotBinOverRegions0.0010.0000.001
preparePool0.0000.0000.001
reCenterPeaks0.0210.0000.021
summarizeOverlapsByBins3.3710.3433.409
summarizePatternInPeaks0.7210.0600.781
tileCount0.3990.2590.559
tileGRanges0.2900.1530.065
toGRanges0.1690.0120.182
translatePattern0.0000.0020.001
wgEncodeTfbsV30.2870.0200.307
write2FASTA0.0260.0000.027
xget0.2110.0080.219