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This page was generated on 2021-08-02 12:04:19 -0400 (Mon, 02 Aug 2021).

CHECK results for ChIPpeakAnno on nebbiolo2

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.
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raw results

Package 290/2015HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPpeakAnno 3.27.4  (landing page)
Jianhong Ou
Snapshot Date: 2021-08-01 14:50:04 -0400 (Sun, 01 Aug 2021)
URL: https://git.bioconductor.org/packages/ChIPpeakAnno
Branch: master
Last Commit: 18eea1a
Last Changed Date: 2021-07-13 08:15:27 -0400 (Tue, 13 Jul 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / 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: 3.27.4
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings ChIPpeakAnno_3.27.4.tar.gz
StartedAt: 2021-08-01 19:02:26 -0400 (Sun, 01 Aug 2021)
EndedAt: 2021-08-01 19:12:42 -0400 (Sun, 01 Aug 2021)
EllapsedTime: 616.2 seconds
RetCode: 0
Status:   OK  
CheckDir: ChIPpeakAnno.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings ChIPpeakAnno_3.27.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/ChIPpeakAnno.Rcheck’
* using R version 4.1.0 beta (2021-05-03 r80259)
* 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 ‘3.27.4’
* 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 ... 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            25.806  0.112  25.919
annotatePeakInBatch      14.990  0.400  15.403
findMotifsInPromoterSeqs 12.137  0.016  12.223
ExonPlusUtr.human.GRCh37  5.696  0.840   6.536
* 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-3.14-bioc/meat/ChIPpeakAnno.Rcheck/00check.log’
for details.



Installation output

ChIPpeakAnno.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL ChIPpeakAnno
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-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 beta (2021-05-03 r80259) -- "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

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")
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (5)

[ FAIL 0 | WARN 3 | SKIP 5 | PASS 313 ]
> 
> proc.time()
   user  system elapsed 
213.833   3.257 219.052 

Example timings

ChIPpeakAnno.Rcheck/ChIPpeakAnno-Ex.timings

nameusersystemelapsed
ChIPpeakAnno-package000
ExonPlusUtr.human.GRCh375.6960.8406.536
HOT.spots0.1280.0120.141
IDRfilter0.0010.0010.001
Peaks.Ste12.Replicate10.0740.0190.095
Peaks.Ste12.Replicate20.0200.0120.033
Peaks.Ste12.Replicate30.0220.0070.030
TSS.human.GRCh370.1940.0350.230
TSS.human.GRCh380.1460.0040.150
TSS.human.NCBI360.1160.0040.119
TSS.mouse.GRCm380.1120.0080.120
TSS.mouse.NCBIM370.0990.0120.111
TSS.rat.RGSC3.40.0810.0130.093
TSS.rat.Rnor_5.00.0680.0070.077
TSS.zebrafish.Zv80.0680.0120.080
TSS.zebrafish.Zv90.1000.0010.100
addAncestors1.2280.0441.272
addGeneIDs1.8270.1151.944
addMetadata1.8280.1561.984
annoGR000
annoPeaks3.5720.1294.861
annotatePeakInBatch14.990 0.40015.403
annotatedPeak0.0660.0000.067
assignChromosomeRegion0.0010.0000.000
bdp000
binOverFeature1.0420.0201.063
binOverGene000
binOverRegions0.0000.0000.001
condenseMatrixByColnames0.0130.0000.013
convert2EntrezID0.380.000.38
countPatternInSeqs0.1560.0000.156
cumulativePercentage000
downstreams0.0320.0000.032
egOrgMap0.0000.0000.001
enrichedGO0.0020.0000.002
enrichmentPlot0.3540.0000.354
estFragmentLength0.0000.0000.001
estLibSize000
featureAlignedDistribution0.2620.0000.261
featureAlignedExtendSignal0.0010.0000.001
featureAlignedHeatmap0.4470.0040.451
featureAlignedSignal0.2280.0160.244
findEnhancers25.806 0.11225.919
findMotifsInPromoterSeqs12.137 0.01612.223
findOverlappingPeaks0.0010.0000.001
findOverlapsOfPeaks2.7190.0042.723
genomicElementDistribution0.0010.0000.001
genomicElementUpSetR0.0010.0000.000
getAllPeakSequence0.6040.0120.616
getAnnotation0.0010.0000.001
getEnrichedGO0.0090.0000.008
getEnrichedPATH0.0010.0000.001
getGO000
getGeneSeq000
getUniqueGOidCount0.0010.0000.001
getVennCounts0.0010.0000.001
hyperGtest0.0010.0000.001
makeVennDiagram0.0010.0000.002
mergePlusMinusPeaks000
metagenePlot2.3250.0402.366
myPeakList0.0170.0020.018
oligoFrequency0.1860.0000.187
oligoSummary000
peakPermTest0.0010.0000.001
peaksNearBDP000
pie10.0050.0000.006
plotBinOverRegions000
preparePool000
reCenterPeaks0.0450.0000.046
summarizeOverlapsByBins3.3310.3313.363
summarizePatternInPeaks0.6690.0440.713
tileCount0.5560.3720.534
tileGRanges0.0870.0080.095
toGRanges0.1200.0240.144
translatePattern0.0010.0000.001
wgEncodeTfbsV30.2300.0080.238
write2FASTA0.0270.0000.028
xget0.1350.0000.136