Package: ngsReports

Version: 1.0.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ngsReports.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ngsReports_1.0.1.tar.gz

StartedAt: 2019-10-16 05:06:29 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 05:13:45 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 436.6 seconds

RetCode: 0

Status:  OK

CheckDir: ngsReports.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ngsReports.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ngsReports_1.0.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/ngsReports.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 ‘ngsReports/DESCRIPTION’ ... OK
* this is package ‘ngsReports’ version ‘1.0.1’
* 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 ‘ngsReports’ can be installed ... OK
* checking installed package size ... OK
* 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 data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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: OK

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ngsReports
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘ngsReports’ ...
** 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 (ngsReports)

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.

> library(testthat)
> library(ngsReports)
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: ggplot2
Loading required package: tibble
> 
> test_check("ngsReports")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 171 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 49.981   4.795  53.729 

name	user	system	elapsed
FastqcData	0.131	0.014	0.152
FastqcDataList	0.598	0.042	0.659
TheoreticalGC-class	0.138	0.011	0.151
dot-FastqcFile-class	0.004	0.002	0.006
dot-addPercent	0	0	0
dot-emptyPlot	0.203	0.012	0.216
dot-makeDendro	0.625	0.029	0.653
dot-makeLabels	0.001	0.001	0.002
dot-splitByTab	0.007	0.001	0.007
estGcDistn	0.039	0.002	0.041
extract-methods	0.578	0.029	0.607
fqName-methods	0.579	0.022	0.601
fqcVersion	0.729	0.026	0.755
gcAvail	0.389	0.050	0.439
gcTheoretical	0.084	0.015	0.098
getColours-methods	0.004	0.001	0.004
getGC	0.034	0.006	0.040
getModule	0.719	0.027	0.746
getSummary	0.451	0.021	0.473
importNgsLogs	0.025	0.000	0.026
isCompressed	0.002	0.001	0.002
mData	0.020	0.000	0.021
maxAdapterContent	0.647	0.024	0.671
overRep2Fasta-methods	0.647	0.024	0.671
path	0.574	0.020	0.594
plotAdapterContent-methods	2.625	0.081	2.708
plotBaseQuals-methods	2.420	0.163	2.584
plotDupLevels-methods	1.852	0.086	1.939
plotGcContent-methods	1.034	0.033	1.067
plotKmers-methods	0.972	0.031	1.003
plotNContent-methods	0.683	0.034	0.719
plotOverrep-methods	1.061	0.018	1.080
plotReadTotals-methods	1.004	0.015	1.021
plotSeqContent-methods	0.933	0.027	0.960
plotSeqLengthDistn-methods	1.765	0.022	1.786
plotSeqQuals-methods	1.585	0.040	1.625
plotSummary-methods	0.995	0.024	1.019
pwf	0.005	0.001	0.007
readTotals	0.654	0.022	0.676
runFastQC-methods	0.001	0.000	0.000
writeHtmlReport	0.000	0.000	0.001