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CHECK report for ATACseqQC on celaya2

This page was generated on 2019-10-16 13:00:11 -0400 (Wed, 16 Oct 2019).

Package 91/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ATACseqQC 1.8.5
Jianhong Ou
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/ATACseqQC
Branch: RELEASE_3_9
Last Commit: 4087212
Last Changed Date: 2019-07-24 09:17:22 -0400 (Wed, 24 Jul 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: ATACseqQC
Version: 1.8.5
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ATACseqQC.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ATACseqQC_1.8.5.tar.gz
StartedAt: 2019-10-16 00:40:15 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 00:52:15 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 719.3 seconds
RetCode: 0
Status:  OK 
CheckDir: ATACseqQC.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ATACseqQC.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ATACseqQC_1.8.5.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/ATACseqQC.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ATACseqQC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ATACseqQC’ version ‘1.8.5’
* 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 ‘ATACseqQC’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 11.2Mb
  sub-directories of 1Mb or more:
    extdata  10.9Mb
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
enrichedFragments     106.336  3.374 109.733
distanceDyad           35.138  1.305  36.466
factorFootprints       28.343  1.103  29.446
vPlot                  25.756  1.153  26.913
splitGAlignmentsByCut  24.846  2.016  26.874
footprintsScanner      23.342  2.029  25.372
shiftGAlignmentsList    7.514  0.989   8.542
estimateLibComplexity   7.220  0.047   7.268
* 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
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/ATACseqQC.Rcheck/00check.log’
for details.



Installation output

ATACseqQC.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘ATACseqQC’ ...
** using staged installation
** R
** 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 (ATACseqQC)

Tests output

ATACseqQC.Rcheck/tests/runTests.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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("ATACseqQC") || stop("unable to load Package:ATACseqQC")
Loading required package: ATACseqQC
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, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    expand.grid


[1] TRUE
> require("GenomicAlignments") || stop("unable to load Package:GenomicAlignments")
Loading required package: GenomicAlignments
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: SummarizedExperiment
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")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply, rowsum

Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    type

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

    strsplit

Loading required package: Rsamtools
[1] TRUE
> require("BSgenome") || stop("unable to load Package:BSgenome")
Loading required package: BSgenome
Loading required package: rtracklayer
[1] TRUE
> require("rtracklayer") || stop("unable to load Package:rtracklayer")
[1] TRUE
> require("utils") || stop("unable to load Package:utils")
[1] TRUE
> require("testthat") || stop("unable to load testthat")
Loading required package: testthat
[1] TRUE
> test_check("ATACseqQC")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 21 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 27.447   2.010  29.923 

Example timings

ATACseqQC.Rcheck/ATACseqQC-Ex.timings

nameusersystemelapsed
NFRscore3.4540.1293.588
PTscore1.2590.0571.316
TSSEscore1.1170.0381.155
bamQC3.4080.3403.749
distanceDyad35.138 1.30536.466
enrichedFragments106.336 3.374109.733
estimateLibComplexity7.2200.0477.268
factorFootprints28.343 1.10329.446
footprintsScanner23.342 2.02925.372
fragSizeDist0.7750.0420.826
plotCorrelation2.3480.0912.440
plotFootprints1.4270.0301.457
prepareBindingSitesList0.5630.0130.575
readBamFile1.4990.1721.671
readsDupFreq0.7090.0590.768
saturationPlot0.0000.0010.000
shiftGAlignmentsList7.5140.9898.542
splitBam0.0030.0010.003
splitGAlignmentsByCut24.846 2.01626.874
vPlot25.756 1.15326.913
writeListOfGAlignments0.6240.0180.642