Package: ngsReports

Version: 1.2.0

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_1.2.0.tar.gz

StartedAt: 2020-04-15 04:15:00 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 04:20:48 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 348.1 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_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/ngsReports.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.2.0’
* 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 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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: 205 | SKIPPED: 0 | WARNINGS: 5 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 45.967   2.893  46.438 

name	user	system	elapsed
FastqcData	0.108	0.005	0.118
FastqcDataList	0.533	0.018	0.561
TheoreticalGC-class	0.194	0.003	0.198
dot-FastqcFile-class	0.003	0.001	0.004
dot-addPercent	0	0	0
dot-emptyPlot	0.151	0.002	0.154
dot-makeDendro	0.461	0.013	0.478
dot-makeLabels	0.001	0.000	0.002
dot-splitByTab	0.006	0.001	0.007
estGcDistn	0.030	0.001	0.031
extract-methods	1.176	0.016	1.202
fqName-methods	0.491	0.011	0.508
fqcVersion	0.536	0.016	0.556
gcAvail	0.329	0.043	0.374
gcTheoretical	0.040	0.005	0.046
getColours-methods	0.002	0.001	0.002
getGC	0.021	0.003	0.024
getModule	0.644	0.036	0.684
getSummary	0.475	0.008	0.487
importNgsLogs	0.038	0.001	0.039
isCompressed	0.002	0.001	0.002
mData	0.023	0.000	0.024
maxAdapterContent	0.543	0.008	0.556
overRep2Fasta-methods	0.572	0.016	0.591
path	0.577	0.012	0.593
plotAdapterContent-methods	2.477	0.096	2.594
plotAlignmentSummary	0.437	0.002	0.441
plotAssemblyStats	0.994	0.006	1.016
plotBaseQuals-methods	1.246	0.013	1.275
plotDupLevels-methods	1.589	0.016	1.613
plotFastqcPCA-methods	1.073	0.014	1.098
plotGcContent-methods	1.066	0.015	1.096
plotKmers-methods	1.009	0.010	1.030
plotNContent-methods	0.659	0.010	0.674
plotOverrep-methods	0.939	0.010	0.955
plotReadTotals-methods	1.050	0.010	1.071
plotSeqContent-methods	0.769	0.009	0.783
plotSeqLengthDistn-methods	1.392	0.008	1.411
plotSeqQuals-methods	1.319	0.013	1.339
plotSummary-methods	0.846	0.009	0.862
pwf	0.006	0.000	0.006
readTotals	0.564	0.009	0.581
runFastQC-methods	0	0	0
writeHtmlReport	0.000	0.000	0.001