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CHECK report for ATACseqQC on tokay1

This page was generated on 2020-08-07 12:11:53 -0400 (Fri, 07 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE ATACseqQC PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 93/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ATACseqQC 1.13.3
Jianhong Ou
Snapshot Date: 2020-08-06 14:50:46 -0400 (Thu, 06 Aug 2020)
URL: https://git.bioconductor.org/packages/ATACseqQC
Branch: master
Last Commit: 2996d20
Last Changed Date: 2020-05-29 21:55:02 -0400 (Fri, 29 May 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ATACseqQC
Version: 1.13.3
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ATACseqQC.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings ATACseqQC_1.13.3.tar.gz
StartedAt: 2020-08-07 03:53:34 -0400 (Fri, 07 Aug 2020)
EndedAt: 2020-08-07 04:09:50 -0400 (Fri, 07 Aug 2020)
EllapsedTime: 975.8 seconds
RetCode: 0
Status:  OK  
CheckDir: ATACseqQC.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ATACseqQC.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings ATACseqQC_1.13.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/ATACseqQC.Rcheck'
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ATACseqQC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ATACseqQC' version '1.13.3'
* 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 whether package 'ATACseqQC' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 11.4Mb
  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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
enrichedFragments     80.46   3.47   84.39
distanceDyad          24.04   0.59   24.63
factorFootprints      22.50   0.27   22.77
vPlot                 22.02   0.35   22.55
splitGAlignmentsByCut 20.42   1.09   24.47
footprintsScanner     17.03   0.44   17.48
shiftGAlignments       9.89   0.59   10.64
shiftGAlignmentsList   6.64   0.33    6.98
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
enrichedFragments     82.72   2.55   85.26
distanceDyad          33.81   0.41   34.22
factorFootprints      26.07   0.31   26.39
splitGAlignmentsByCut 25.15   1.23   27.53
vPlot                 22.45   0.32   22.77
footprintsScanner     21.70   0.44   22.15
shiftGAlignments      10.24   0.50   10.77
shiftGAlignmentsList   6.18   0.17    6.35
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/ATACseqQC.Rcheck/00check.log'
for details.



Installation output

ATACseqQC.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/ATACseqQC_1.13.3.tar.gz && rm -rf ATACseqQC.buildbin-libdir && mkdir ATACseqQC.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ATACseqQC.buildbin-libdir ATACseqQC_1.13.3.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL ATACseqQC_1.13.3.zip && rm ATACseqQC_1.13.3.tar.gz ATACseqQC_1.13.3.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 81 11.0M   81 9200k    0     0  64.3M      0 --:--:-- --:--:-- --:--:-- 65.5M
100 11.0M  100 11.0M    0     0  68.5M      0 --:--:-- --:--:-- --:--:-- 69.7M

install for i386

* installing *source* package 'ATACseqQC' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
No methods found in package 'IRanges' for request: 'values' when loading 'GenomicScores'
** help
*** installing help indices
  converting help for package 'ATACseqQC'
    finding HTML links ... done
    ATACseqQC-package                       html  
    DB                                      html  
    NFRscore                                html  
    PTscore                                 html  
    TSSEscore                               html  
    bamQC                                   html  
    distanceDyad                            html  
    enrichedFragments                       html  
    estimateLibComplexity                   html  
    factorFootprints                        html  
    footprintsScanner                       html  
    fragSizeDist                            html  
    peakdet                                 html  
    plotCorrelation                         html  
    plotFootprints                          html  
    pwmscores                               html  
    readBamFile                             html  
    finding level-2 HTML links ... done

    readsDupFreq                            html  
    saturationPlot                          html  
    shiftGAlignments                        html  
    shiftGAlignmentsList                    html  
    shiftReads                              html  
    splitBam                                html  
    splitGAlignmentsByCut                   html  
    vPlot                                   html  
    writeListOfGAlignments                  html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package 'IRanges' for request: 'values' when loading 'GenomicScores'
** testing if installed package can be loaded from final location
No methods found in package 'IRanges' for request: 'values' when loading 'GenomicScores'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'ATACseqQC' ...
** testing if installed package can be loaded
No methods found in package 'IRanges' for request: 'values' when loading 'GenomicScores'
* MD5 sums
packaged installation of 'ATACseqQC' as ATACseqQC_1.13.3.zip
* DONE (ATACseqQC)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'ATACseqQC' successfully unpacked and MD5 sums checked

Tests output

ATACseqQC.Rcheck/tests_i386/runTests.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    expand.grid

No methods found in package 'IRanges' for request: 'values' when loading 'GenomicScores'
[1] TRUE
> require("GenomicAlignments") || stop("unable to load Package:GenomicAlignments")
Loading required package: GenomicAlignments
Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

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: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand

Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians


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: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 
  20.65    2.09   22.76 

ATACseqQC.Rcheck/tests_x64/runTests.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    expand.grid

No methods found in package 'IRanges' for request: 'values' when loading 'GenomicScores'
[1] TRUE
> require("GenomicAlignments") || stop("unable to load Package:GenomicAlignments")
Loading required package: GenomicAlignments
Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

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: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand

Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians


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: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 
  26.21    0.85   27.64 

Example timings

ATACseqQC.Rcheck/examples_i386/ATACseqQC-Ex.timings

nameusersystemelapsed
NFRscore1.420.191.64
PTscore0.810.020.83
TSSEscore0.670.010.69
bamQC2.230.182.53
distanceDyad24.04 0.5924.63
enrichedFragments80.46 3.4784.39
estimateLibComplexity4.820.114.94
factorFootprints22.50 0.2722.77
footprintsScanner17.03 0.4417.48
fragSizeDist0.680.031.90
plotCorrelation1.540.031.58
plotFootprints0.830.060.92
readBamFile1.060.201.27
readsDupFreq0.630.100.72
saturationPlot000
shiftGAlignments 9.89 0.5910.64
shiftGAlignmentsList6.640.336.98
splitBam000
splitGAlignmentsByCut20.42 1.0924.47
vPlot22.02 0.3522.55
writeListOfGAlignments0.220.010.24

ATACseqQC.Rcheck/examples_x64/ATACseqQC-Ex.timings

nameusersystemelapsed
NFRscore2.670.082.75
PTscore2.500.082.58
TSSEscore1.110.041.15
bamQC3.350.113.45
distanceDyad33.81 0.4134.22
enrichedFragments82.72 2.5585.26
estimateLibComplexity4.120.044.17
factorFootprints26.07 0.3126.39
footprintsScanner21.70 0.4422.15
fragSizeDist0.590.020.61
plotCorrelation1.500.041.55
plotFootprints0.690.020.70
readBamFile0.900.060.96
readsDupFreq0.420.020.44
saturationPlot000
shiftGAlignments10.24 0.5010.77
shiftGAlignmentsList6.180.176.35
splitBam000
splitGAlignmentsByCut25.15 1.2327.53
vPlot22.45 0.3222.77
writeListOfGAlignments0.250.010.27