Back to Multiple platform build/check report for BioC 3.17:   simplified   long
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2023-02-07 11:05:07 -0500 (Tue, 07 Feb 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4483
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-01-10 r83596 ucrt) -- "Unsuffered Consequences" 4249
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4272
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? 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 308/2164HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPpeakAnno 3.33.1  (landing page)
Jianhong Ou
Snapshot Date: 2023-02-06 14:00:21 -0500 (Mon, 06 Feb 2023)
git_url: https://git.bioconductor.org/packages/ChIPpeakAnno
git_branch: master
git_last_commit: 2c08eb8
git_last_commit_date: 2022-11-12 17:40:09 -0500 (Sat, 12 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / 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: 3.33.1
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings ChIPpeakAnno_3.33.1.tar.gz
StartedAt: 2023-02-06 19:39:46 -0500 (Mon, 06 Feb 2023)
EndedAt: 2023-02-06 19:55:47 -0500 (Mon, 06 Feb 2023)
EllapsedTime: 960.5 seconds
RetCode: 0
Status:   OK  
CheckDir: ChIPpeakAnno.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings ChIPpeakAnno_3.33.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/ChIPpeakAnno.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘ChIPpeakAnno/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChIPpeakAnno’ version ‘3.33.1’
* 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 17.4Mb
  sub-directories of 1Mb or more:
    data     12.6Mb
    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 ... NOTE
Namespace in Imports field not imported from: ‘ensembldb’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
oligoFrequency : <anonymous>: no visible global function definition for
  ‘oligonucleotideFrequency’
Undefined global functions or variables:
  oligonucleotideFrequency
* checking Rd files ... NOTE
checkRd: (-1) assignChromosomeRegion.Rd:133: Escaped LaTeX specials: \_
* 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            21.213  0.304  21.518
findMotifsInPromoterSeqs 12.995  0.248  13.244
annotatePeakInBatch      11.852  0.535  12.401
summarizeOverlapsByBins   5.534  0.497   5.757
* 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 ...
  ‘ChIPpeakAnno.Rmd’ using ‘UTF-8’... OK
  ‘FAQs.Rmd’ using ‘UTF-8’... OK
  ‘pipeline.Rmd’ using ‘UTF-8’... OK
  ‘quickStart.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/ChIPpeakAnno.Rcheck/00check.log’
for details.



Installation output

ChIPpeakAnno.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL ChIPpeakAnno
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-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
in method for ‘annoGR’ with signature ‘"EnsDb"’: no definition for class “EnsDb”
in method for ‘toGRanges’ with signature ‘"EnsDb"’: no definition for class “EnsDb”
** 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) (2023-01-10 r83596) -- "Unsuffered Consequences"
Copyright (C) 2023 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, aperm, 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 4 | SKIP 6 | PASS 316 ]

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

[ FAIL 0 | WARN 4 | SKIP 6 | PASS 316 ]
> 
> proc.time()
   user  system elapsed 
169.406   4.283 175.753 

Example timings

ChIPpeakAnno.Rcheck/ChIPpeakAnno-Ex.timings

nameusersystemelapsed
ChIPpeakAnno-package000
ExonPlusUtr.human.GRCh373.2510.2043.455
HOT.spots0.1260.0200.147
IDRfilter0.0000.0010.001
Peaks.Ste12.Replicate10.0500.0020.051
Peaks.Ste12.Replicate20.0120.0000.013
Peaks.Ste12.Replicate30.0050.0080.013
TSS.human.GRCh370.2050.0120.217
TSS.human.GRCh380.1580.0000.159
TSS.human.NCBI360.0940.0160.109
TSS.mouse.GRCm380.1040.0000.105
TSS.mouse.NCBIM370.0910.0080.100
TSS.rat.RGSC3.40.0680.0120.080
TSS.rat.Rnor_5.00.0670.0040.070
TSS.zebrafish.Zv80.0650.0080.072
TSS.zebrafish.Zv90.0860.0200.107
addAncestors1.0200.0641.085
addGeneIDs1.6530.1791.834
addMetadata1.2960.1481.444
annoGR000
annoPeaks3.0390.2673.922
annotatePeakInBatch11.852 0.53512.401
annotatedPeak0.0500.0080.058
assignChromosomeRegion0.0010.0000.001
bdp0.0010.0010.001
binOverFeature0.7010.0070.709
binOverGene0.0000.0000.001
binOverRegions0.0010.0000.001
condenseMatrixByColnames0.0110.0000.010
convert2EntrezID0.3040.0080.311
countPatternInSeqs0.1470.0080.156
cumulativePercentage0.0000.0000.001
downstreams0.0220.0000.022
egOrgMap0.0010.0000.000
enrichedGO0.0020.0000.002
enrichmentPlot0.5480.0040.553
estFragmentLength0.0000.0000.001
estLibSize0.0000.0000.001
featureAlignedDistribution0.2160.0000.216
featureAlignedExtendSignal0.0020.0000.001
featureAlignedHeatmap0.2980.0080.305
featureAlignedSignal0.1830.0560.238
findEnhancers21.213 0.30421.518
findMotifsInPromoterSeqs12.995 0.24813.244
findOverlappingPeaks0.0010.0000.001
findOverlapsOfPeaks1.8090.0041.814
genomicElementDistribution0.0010.0000.001
genomicElementUpSetR0.0010.0000.000
getAllPeakSequence0.6920.0240.717
getAnnotation0.0020.0000.001
getEnrichedGO0.0090.0030.010
getEnrichedPATH0.0000.0000.001
getGO0.0000.0000.001
getGeneSeq0.0010.0000.001
getUniqueGOidCount0.0000.0000.001
getVennCounts0.0010.0000.001
hyperGtest0.0010.0000.001
makeVennDiagram0.0030.0000.002
mergePlusMinusPeaks0.0010.0000.000
metagenePlot2.1840.0362.222
myPeakList0.0160.0000.016
oligoFrequency0.1730.0120.184
oligoSummary0.0000.0000.001
peakPermTest0.0010.0000.002
peaksNearBDP0.0000.0000.001
pie10.0050.0000.005
plotBinOverRegions0.0010.0000.001
preparePool0.0000.0000.001
reCenterPeaks0.0250.0000.026
summarizeOverlapsByBins5.5340.4975.757
summarizePatternInPeaks0.5460.0200.567
tileCount0.2170.1830.338
tileGRanges0.1820.1050.065
toGRanges0.0890.0160.105
translatePattern0.0010.0000.001
wgEncodeTfbsV30.2100.0160.225
write2FASTA0.0130.0040.016
xget0.1190.0040.122