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CHECK report for ATACseqQC on merida2

This page was generated on 2019-04-09 13:35:01 -0400 (Tue, 09 Apr 2019).

Package 89/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ATACseqQC 1.7.8
Jianhong Ou
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/ATACseqQC
Branch: master
Last Commit: e7620f3
Last Changed Date: 2019-02-01 15:36:43 -0400 (Fri, 01 Feb 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK 

Summary

Package: ATACseqQC
Version: 1.7.8
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_1.7.8.tar.gz
StartedAt: 2019-04-08 23:19:05 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 23:28:25 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 559.8 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_1.7.8.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/ATACseqQC.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.7.8’
* 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     85.604  1.711  88.032
distanceDyad          32.138  0.620  33.091
factorFootprints      28.711  0.657  29.626
vPlot                 25.511  0.526  26.327
footprintsScanner     16.689  0.876  17.674
splitGAlignmentsByCut 11.782  0.947  12.790
shiftGAlignmentsList   6.982  0.515   7.578
estimateLibComplexity  5.584  0.097   5.735
* 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’ ...
** 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
* DONE (ATACseqQC)

Tests output

ATACseqQC.Rcheck/tests/runTests.Rout


R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 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, colMeans, colSums, 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, rowMeans, rowSums,
    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 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 19.343   0.869  20.341 

Example timings

ATACseqQC.Rcheck/ATACseqQC-Ex.timings

nameusersystemelapsed
NFRscore1.6360.0491.705
PTscore1.7360.0251.775
TSSEscore0.8220.0590.890
bamQC2.6660.1032.787
distanceDyad32.138 0.62033.091
enrichedFragments85.604 1.71188.032
estimateLibComplexity5.5840.0975.735
factorFootprints28.711 0.65729.626
footprintsScanner16.689 0.87617.674
fragSizeDist0.5830.0190.606
plotCorrelation1.4110.0501.473
plotFootprints0.9310.0060.947
prepareBindingSitesList0.2850.0060.295
readBamFile1.0250.0661.097
readsDupFreq0.5570.0390.600
saturationPlot0.0000.0000.001
shiftGAlignmentsList6.9820.5157.578
splitBam0.0020.0010.002
splitGAlignmentsByCut11.782 0.94712.790
vPlot25.511 0.52626.327
writeListOfGAlignments0.3870.0090.398