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This page was generated on 2023-01-28 11:08:26 -0500 (Sat, 28 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4465
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-01-10 r83596 ucrt) -- "Unsuffered Consequences" 4246
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4269
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 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? 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 307/2162HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPpeakAnno 3.33.1  (landing page)
Jianhong Ou
Snapshot Date: 2023-01-27 14:00:19 -0500 (Fri, 27 Jan 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: /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_3.33.1.tar.gz
StartedAt: 2023-01-27 23:29:40 -0500 (Fri, 27 Jan 2023)
EndedAt: 2023-01-27 23:54:46 -0500 (Fri, 27 Jan 2023)
EllapsedTime: 1505.6 seconds
RetCode: 0
Status:   OK  
CheckDir: ChIPpeakAnno.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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_3.33.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/ChIPpeakAnno.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
    Apple clang version 12.0.0 (clang-1200.0.32.29)
    GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChIPpeakAnno/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChIPpeakAnno’ version ‘3.33.1’
* 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 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 ... 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            48.341  0.575  67.986
findMotifsInPromoterSeqs 29.360  0.259  43.855
annotatePeakInBatch      24.437  0.700  35.383
summarizeOverlapsByBins   5.932  0.582   8.579
annoPeaks                 6.100  0.366  10.008
ExonPlusUtr.human.GRCh37  4.285  0.155   6.481
addGeneIDs                3.500  0.718   6.080
metagenePlot              3.893  0.066   5.839
findOverlapsOfPeaks       3.768  0.024   5.693
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-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/4.3/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
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-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, 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 
345.549   7.107 524.431 

Example timings

ChIPpeakAnno.Rcheck/ChIPpeakAnno-Ex.timings

nameusersystemelapsed
ChIPpeakAnno-package0.0000.0000.001
ExonPlusUtr.human.GRCh374.2850.1556.481
HOT.spots0.2150.0180.330
IDRfilter0.0010.0000.002
Peaks.Ste12.Replicate10.0980.0030.157
Peaks.Ste12.Replicate20.0250.0030.036
Peaks.Ste12.Replicate30.0230.0020.030
TSS.human.GRCh370.2650.0390.425
TSS.human.GRCh380.2140.0190.338
TSS.human.NCBI360.1590.0140.251
TSS.mouse.GRCm380.1480.0140.232
TSS.mouse.NCBIM370.1360.0110.205
TSS.rat.RGSC3.40.1120.0110.184
TSS.rat.Rnor_5.00.1020.0080.157
TSS.zebrafish.Zv80.1060.0100.165
TSS.zebrafish.Zv90.1290.0090.196
addAncestors2.3510.1013.513
addGeneIDs3.5000.7186.080
addMetadata2.8120.2344.321
annoGR000
annoPeaks 6.100 0.36610.008
annotatePeakInBatch24.437 0.70035.383
annotatedPeak0.0930.0060.138
assignChromosomeRegion0.0030.0000.003
bdp0.0000.0000.001
binOverFeature1.5430.0212.061
binOverGene0.0010.0010.002
binOverRegions0.0010.0000.002
condenseMatrixByColnames0.0220.0000.030
convert2EntrezID0.6730.0050.924
countPatternInSeqs0.2930.0060.409
cumulativePercentage0.0000.0000.001
downstreams0.0460.0000.064
egOrgMap0.0010.0000.001
enrichedGO0.0030.0040.006
enrichmentPlot1.1510.0211.544
estFragmentLength0.0000.0000.001
estLibSize0.0010.0000.001
featureAlignedDistribution0.4580.0020.604
featureAlignedExtendSignal0.0030.0000.004
featureAlignedHeatmap0.6590.0030.886
featureAlignedSignal0.3820.0390.590
findEnhancers48.341 0.57567.986
findMotifsInPromoterSeqs29.360 0.25943.855
findOverlappingPeaks0.0020.0010.002
findOverlapsOfPeaks3.7680.0245.693
genomicElementDistribution0.0040.0000.004
genomicElementUpSetR0.0010.0010.002
getAllPeakSequence0.9880.0251.449
getAnnotation0.0030.0010.003
getEnrichedGO0.0190.0050.035
getEnrichedPATH0.0010.0010.002
getGO0.0000.0000.001
getGeneSeq0.0030.0010.003
getUniqueGOidCount0.0010.0000.001
getVennCounts0.0020.0000.002
hyperGtest0.0020.0000.002
makeVennDiagram0.0060.0010.006
mergePlusMinusPeaks0.0010.0010.004
metagenePlot3.8930.0665.839
myPeakList0.0220.0020.031
oligoFrequency0.3080.0120.470
oligoSummary0.0010.0010.001
peakPermTest0.0020.0000.002
peaksNearBDP0.0010.0000.001
pie10.0100.0010.016
plotBinOverRegions0.0010.0000.001
preparePool0.0010.0000.001
reCenterPeaks0.0500.0000.073
summarizeOverlapsByBins5.9320.5828.579
summarizePatternInPeaks0.9630.0871.500
tileCount0.7090.4960.901
tileGRanges0.0760.0120.103
toGRanges0.2310.0230.367
translatePattern0.0010.0000.001
wgEncodeTfbsV30.3350.0170.509
write2FASTA0.0330.0050.046
xget0.1580.0130.244