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CHECK report for ATACseqQC on malbec2

This page was generated on 2018-10-17 08:30:14 -0400 (Wed, 17 Oct 2018).

Package 80/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ATACseqQC 1.4.3
Jianhong Ou
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/ATACseqQC
Branch: RELEASE_3_7
Last Commit: 29b48ac
Last Changed Date: 2018-09-27 12:50:36 -0400 (Thu, 27 Sep 2018)
malbec2 Linux (Ubuntu 16.04.1 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ATACseqQC
Version: 1.4.3
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:ATACseqQC.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings ATACseqQC_1.4.3.tar.gz
StartedAt: 2018-10-15 22:33:34 -0400 (Mon, 15 Oct 2018)
EndedAt: 2018-10-15 22:40:18 -0400 (Mon, 15 Oct 2018)
EllapsedTime: 403.9 seconds
RetCode: 0
Status:  OK 
CheckDir: ATACseqQC.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:ATACseqQC.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings ATACseqQC_1.4.3.tar.gz
###
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##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/ATACseqQC.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (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 ‘1.4.3’
* 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     64.560  0.332  65.003
footprintsScanner     24.844  0.368  25.228
distanceDyad          17.868  0.336  18.226
factorFootprints      16.692  0.880  17.654
vPlot                 14.392  0.228  14.628
splitGAlignmentsByCut  7.080  0.296   7.385
* 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-3.7-bioc/meat/ATACseqQC.Rcheck/00check.log’
for details.



Installation output

ATACseqQC.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL ATACseqQC
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/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 version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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("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, lengths, 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

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 
 13.844   0.360  14.704 

Example timings

ATACseqQC.Rcheck/ATACseqQC-Ex.timings

nameusersystemelapsed
NFRscore1.1680.0361.235
PTscore0.6720.0080.682
bamQC2.7000.0362.757
distanceDyad17.868 0.33618.226
enrichedFragments64.560 0.33265.003
estimateLibComplexity3.8720.0003.888
factorFootprints16.692 0.88017.654
footprintsScanner24.844 0.36825.228
fragSizeDist0.6880.0040.722
plotCorrelation1.0880.0081.095
plotFootprints0.5960.0000.597
prepareBindingSitesList0.2680.0000.269
readBamFile0.9320.0000.935
readsDupFreq0.3800.0080.387
saturationPlot0.0000.0000.001
shiftGAlignmentsList4.5520.1684.726
splitBam0.0040.0000.001
splitGAlignmentsByCut7.0800.2967.385
vPlot14.392 0.22814.628
writeListOfGAlignments0.2600.0040.266