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This page was generated on 2021-06-21 14:05:42 -0400 (Mon, 21 Jun 2021).

CHECK results for ChIPpeakAnno on machv2

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 294/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPpeakAnno 3.26.0  (landing page)
Jianhong Ou
Snapshot Date: 2021-06-20 06:50:09 -0400 (Sun, 20 Jun 2021)
URL: https://git.bioconductor.org/packages/ChIPpeakAnno
Branch: RELEASE_3_13
Last Commit: 13852b2
Last Changed Date: 2021-05-19 11:43:39 -0400 (Wed, 19 May 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: 3.26.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ChIPpeakAnno_3.26.0.tar.gz
StartedAt: 2021-06-20 16:58:50 -0400 (Sun, 20 Jun 2021)
EndedAt: 2021-06-20 17:10:40 -0400 (Sun, 20 Jun 2021)
EllapsedTime: 710.2 seconds
RetCode: 0
Status:   OK  
CheckDir: ChIPpeakAnno.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ChIPpeakAnno_3.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/ChIPpeakAnno.Rcheck’
* using R version 4.1.0 (2021-05-18)
* using platform: x86_64-apple-darwin17.0 (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 ‘3.26.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 19.6Mb
  sub-directories of 1Mb or more:
    data     13.1Mb
    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            40.788  0.389  41.204
findMotifsInPromoterSeqs 19.646  0.171  19.926
annotatePeakInBatch      17.919  0.378  18.307
annoPeaks                 3.957  0.278   6.211
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/ChIPpeakAnno.Rcheck/00check.log’
for details.



Installation output

ChIPpeakAnno.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ChIPpeakAnno
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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
** 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-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
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 
165.895   3.266 172.565 

Example timings

ChIPpeakAnno.Rcheck/ChIPpeakAnno-Ex.timings

nameusersystemelapsed
ChIPpeakAnno-package0.0010.0010.001
ExonPlusUtr.human.GRCh373.6130.1153.731
HOT.spots0.2040.0150.218
IDRfilter0.0010.0010.002
Peaks.Ste12.Replicate10.1030.0040.106
Peaks.Ste12.Replicate20.0340.0040.037
Peaks.Ste12.Replicate30.0380.0030.041
TSS.human.GRCh370.1870.0160.203
TSS.human.GRCh380.1850.0160.215
TSS.human.NCBI360.1320.0070.139
TSS.mouse.GRCm380.1290.0160.144
TSS.mouse.NCBIM370.1110.0120.123
TSS.rat.RGSC3.40.1030.0110.114
TSS.rat.Rnor_5.00.0950.0100.104
TSS.zebrafish.Zv80.0940.0090.102
TSS.zebrafish.Zv90.0950.0090.104
addAncestors1.8330.0691.903
addGeneIDs2.6720.5843.259
addMetadata2.8060.0532.861
annoGR0.0010.0010.000
annoPeaks3.9570.2786.211
annotatePeakInBatch17.919 0.37818.307
annotatedPeak0.0710.0020.073
assignChromosomeRegion0.0020.0000.002
bdp0.0000.0000.001
binOverFeature1.6040.0221.628
binOverGene0.0010.0000.001
binOverRegions0.0000.0010.001
condenseMatrixByColnames0.0140.0010.014
convert2EntrezID1.5840.0221.606
countPatternInSeqs0.2170.0050.222
cumulativePercentage0.0000.0010.000
downstreams0.0670.0010.068
egOrgMap0.0010.0010.001
enrichedGO0.0030.0040.006
enrichmentPlot0.5650.0070.572
estFragmentLength0.0000.0000.001
estLibSize0.0000.0000.001
featureAlignedDistribution0.4520.0110.464
featureAlignedExtendSignal0.0030.0010.004
featureAlignedHeatmap0.6310.0560.688
featureAlignedSignal0.4150.1270.543
findEnhancers40.788 0.38941.204
findMotifsInPromoterSeqs19.646 0.17119.926
findOverlappingPeaks0.0010.0000.002
findOverlapsOfPeaks0.9940.0081.003
genomicElementDistribution0.0030.0010.004
genomicElementUpSetR0.0020.0010.002
getAllPeakSequence0.9590.0170.980
getAnnotation0.0020.0020.004
getEnrichedGO0.0150.0070.022
getEnrichedPATH0.0020.0010.002
getGO0.0000.0010.001
getGeneSeq0.0030.0010.003
getUniqueGOidCount0.0010.0010.002
getVennCounts0.0010.0010.001
hyperGtest0.0010.0010.002
makeVennDiagram0.0050.0010.006
mergePlusMinusPeaks0.0010.0010.001
metagenePlot3.0810.0643.150
myPeakList0.0160.0030.019
oligoFrequency0.2090.0140.223
oligoSummary0.0000.0010.001
peakPermTest0.0010.0010.002
peaksNearBDP0.0010.0000.001
pie10.0070.0010.007
plotBinOverRegions0.0010.0010.002
preparePool0.0000.0000.001
reCenterPeaks0.0710.0010.072
summarizeOverlapsByBins3.4350.6563.503
summarizePatternInPeaks1.0670.0921.160
tileCount0.8690.6350.886
tileGRanges0.0940.0150.110
toGRanges0.2620.0310.293
translatePattern000
wgEncodeTfbsV30.2620.0120.273
write2FASTA0.0300.0040.034
xget0.1460.0120.158