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This page was generated on 2021-07-30 15:05:25 -0400 (Fri, 30 Jul 2021).

CHECK results for ChIPpeakAnno on nebbiolo1

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raw results

Package 294/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPpeakAnno 3.26.2  (landing page)
Jianhong Ou
Snapshot Date: 2021-07-29 04:50:02 -0400 (Thu, 29 Jul 2021)
URL: https://git.bioconductor.org/packages/ChIPpeakAnno
Branch: RELEASE_3_13
Last Commit: da90a6c
Last Changed Date: 2021-07-13 11:27:12 -0400 (Tue, 13 Jul 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: 3.26.2
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings ChIPpeakAnno_3.26.2.tar.gz
StartedAt: 2021-07-29 09:18:06 -0400 (Thu, 29 Jul 2021)
EndedAt: 2021-07-29 09:26:52 -0400 (Thu, 29 Jul 2021)
EllapsedTime: 526.5 seconds
RetCode: 0
Status:   OK  
CheckDir: ChIPpeakAnno.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings ChIPpeakAnno_3.26.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/ChIPpeakAnno.Rcheck’
* using R version 4.1.0 (2021-05-18)
* 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 ‘3.26.2’
* 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 ... 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            27.696  0.292  27.989
annotatePeakInBatch      15.382  0.404  15.787
findMotifsInPromoterSeqs 12.796  0.132  12.929
* 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-3.13-bioc/meat/ChIPpeakAnno.Rcheck/00check.log’
for details.



Installation output

ChIPpeakAnno.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL ChIPpeakAnno
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-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 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 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
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 (5)

[ FAIL 0 | WARN 1 | SKIP 5 | PASS 214 ]
> 
> proc.time()
   user  system elapsed 
115.538   5.007 122.449 

Example timings

ChIPpeakAnno.Rcheck/ChIPpeakAnno-Ex.timings

nameusersystemelapsed
ChIPpeakAnno-package000
ExonPlusUtr.human.GRCh374.0520.1564.208
HOT.spots0.1370.0040.141
IDRfilter0.0010.0000.000
Peaks.Ste12.Replicate10.0590.0000.059
Peaks.Ste12.Replicate20.0210.0000.021
Peaks.Ste12.Replicate30.0210.0000.021
TSS.human.GRCh370.2130.0040.217
TSS.human.GRCh380.1660.0000.166
TSS.human.NCBI360.0990.0120.111
TSS.mouse.GRCm380.1090.0000.109
TSS.mouse.NCBIM370.0930.0080.102
TSS.rat.RGSC3.40.0730.0080.081
TSS.rat.Rnor_5.00.0660.0040.070
TSS.zebrafish.Zv80.0740.0000.074
TSS.zebrafish.Zv90.0780.0080.086
addAncestors1.1160.0281.144
addGeneIDs1.6960.1851.882
addMetadata1.8270.0521.879
annoGR0.0000.0000.001
annoPeaks2.7400.2883.922
annotatePeakInBatch15.382 0.40415.787
annotatedPeak0.0640.0080.072
assignChromosomeRegion0.0010.0000.001
bdp0.0000.0010.000
binOverFeature2.6650.0552.720
binOverGene0.0010.0000.000
binOverRegions0.0000.0000.001
condenseMatrixByColnames0.0120.0030.015
convert2EntrezID0.3770.0040.382
countPatternInSeqs0.1910.0000.191
cumulativePercentage000
downstreams0.0460.0000.047
egOrgMap0.0010.0000.000
enrichedGO0.0020.0000.003
enrichmentPlot0.4100.0120.422
estFragmentLength0.0010.0000.001
estLibSize0.0010.0000.000
featureAlignedDistribution0.2980.0000.297
featureAlignedExtendSignal0.0010.0000.002
featureAlignedHeatmap0.4140.0240.437
featureAlignedSignal0.2510.1240.375
findEnhancers27.696 0.29227.989
findMotifsInPromoterSeqs12.796 0.13212.929
findOverlappingPeaks0.0010.0000.001
findOverlapsOfPeaks2.7500.0042.754
genomicElementDistribution0.0010.0000.001
genomicElementUpSetR0.0000.0000.001
getAllPeakSequence0.740.000.74
getAnnotation0.0010.0000.001
getEnrichedGO0.0130.0000.013
getEnrichedPATH0.0000.0000.001
getGO0.0010.0000.000
getGeneSeq0.0000.0010.001
getUniqueGOidCount0.0000.0010.002
getVennCounts0.0010.0000.002
hyperGtest0.0020.0000.002
makeVennDiagram0.0030.0000.002
mergePlusMinusPeaks0.0000.0010.001
metagenePlot2.6510.0702.724
myPeakList0.0150.0000.015
oligoFrequency0.1580.0160.174
oligoSummary0.0010.0000.001
peakPermTest0.0010.0000.001
peaksNearBDP0.0000.0000.001
pie10.0030.0020.005
plotBinOverRegions0.0010.0000.000
preparePool0.0010.0000.001
reCenterPeaks0.0410.0000.041
summarizeOverlapsByBins3.6060.3043.565
summarizePatternInPeaks0.6780.0320.711
tileCount0.3030.1820.432
tileGRanges0.2310.1390.053
toGRanges0.1320.0080.141
translatePattern0.0010.0000.001
wgEncodeTfbsV30.2210.0070.228
write2FASTA0.0230.0000.023
xget0.0970.0080.106