Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-05-20 12:06:18 -0400 (Fri, 20 May 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4155
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
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 palomino3


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 310/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPpeakAnno 3.30.0  (landing page)
Jianhong Ou
Snapshot Date: 2022-05-19 13:55:15 -0400 (Thu, 19 May 2022)
git_url: https://git.bioconductor.org/packages/ChIPpeakAnno
git_branch: RELEASE_3_15
git_last_commit: f5b7c4e
git_last_commit_date: 2022-04-26 11:03:21 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 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: 3.30.0
Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ChIPpeakAnno.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings ChIPpeakAnno_3.30.0.tar.gz
StartedAt: 2022-05-19 22:47:46 -0400 (Thu, 19 May 2022)
EndedAt: 2022-05-19 22:59:45 -0400 (Thu, 19 May 2022)
EllapsedTime: 718.8 seconds
RetCode: 0
Status:   OK  
CheckDir: ChIPpeakAnno.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ChIPpeakAnno.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings ChIPpeakAnno_3.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/ChIPpeakAnno.Rcheck'
* using R version 4.2.0 (2022-04-22 ucrt)
* using platform: x86_64-w64-mingw32 (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 '3.30.0'
* 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 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 ... 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            25.39   0.66   26.06
annotatePeakInBatch      15.81   0.64   16.47
findMotifsInPromoterSeqs 15.81   0.16   21.02
annoPeaks                 3.77   0.36    5.34
summarizeOverlapsByBins   3.14   0.04   21.37
tileCount                 1.38   0.02   18.89
* 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
  'F:/biocbuild/bbs-3.15-bioc/meat/ChIPpeakAnno.Rcheck/00check.log'
for details.



Installation output

ChIPpeakAnno.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL ChIPpeakAnno
###
##############################################################################
##############################################################################


* installing to library 'F:/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 version 4.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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


Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

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")
Error in x$.self$finalize() : attempt to apply non-function
[ FAIL 0 | WARN 3 | SKIP 6 | PASS 313 ]

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

[ FAIL 0 | WARN 3 | SKIP 6 | PASS 313 ]
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
 183.53    6.14  214.09 

Example timings

ChIPpeakAnno.Rcheck/ChIPpeakAnno-Ex.timings

nameusersystemelapsed
ChIPpeakAnno-package000
ExonPlusUtr.human.GRCh374.000.044.04
HOT.spots0.160.000.16
IDRfilter000
Peaks.Ste12.Replicate10.060.020.07
Peaks.Ste12.Replicate20.020.020.03
Peaks.Ste12.Replicate30.000.010.02
TSS.human.GRCh370.200.030.23
TSS.human.GRCh380.140.020.16
TSS.human.NCBI360.110.000.11
TSS.mouse.GRCm380.100.010.11
TSS.mouse.NCBIM370.070.020.09
TSS.rat.RGSC3.40.080.000.08
TSS.rat.Rnor_5.00.060.000.06
TSS.zebrafish.Zv80.070.010.08
TSS.zebrafish.Zv90.090.020.11
addAncestors1.030.011.04
addGeneIDs2.531.003.55
addMetadata1.530.241.77
annoGR000
annoPeaks3.770.365.34
annotatePeakInBatch15.81 0.6416.47
annotatedPeak0.050.000.05
assignChromosomeRegion000
bdp000
binOverFeature1.100.031.14
binOverGene000
binOverRegions000
condenseMatrixByColnames0.020.000.01
convert2EntrezID0.480.010.50
countPatternInSeqs0.220.030.25
cumulativePercentage000
downstreams0.040.000.03
egOrgMap000
enrichedGO0.000.020.02
enrichmentPlot0.50.00.5
estFragmentLength0.010.000.01
estLibSize000
featureAlignedDistribution0.330.020.35
featureAlignedExtendSignal000
featureAlignedHeatmap0.390.000.39
featureAlignedSignal0.270.040.31
findEnhancers25.39 0.6626.06
findMotifsInPromoterSeqs15.81 0.1621.02
findOverlappingPeaks000
findOverlapsOfPeaks2.480.042.53
genomicElementDistribution000
genomicElementUpSetR000
getAllPeakSequence0.580.000.62
getAnnotation000
getEnrichedGO0.020.000.02
getEnrichedPATH000
getGO000
getGeneSeq000
getUniqueGOidCount0.000.020.00
getVennCounts000
hyperGtest000
makeVennDiagram000
mergePlusMinusPeaks000
metagenePlot2.670.142.96
myPeakList0.020.000.02
oligoFrequency0.270.010.28
oligoSummary000
peakPermTest000
peaksNearBDP000
pie10.010.000.02
plotBinOverRegions000
preparePool000
reCenterPeaks0.030.000.03
summarizeOverlapsByBins 3.14 0.0421.37
summarizePatternInPeaks0.530.010.55
tileCount 1.38 0.0218.89
tileGRanges0.030.000.04
toGRanges0.070.010.09
translatePattern000
wgEncodeTfbsV30.180.000.17
write2FASTA0.010.000.02
xget0.110.000.11