Package: ngsReports

Version: 1.0.1

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ngsReports.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ngsReports_1.0.1.tar.gz

StartedAt: 2019-10-16 03:34:05 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 03:39:03 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 297.9 seconds

RetCode: 0

Status:  OK

CheckDir: ngsReports.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ngsReports.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ngsReports_1.0.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/ngsReports.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (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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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL ngsReports
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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-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.

> 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 
 35.958   0.980  38.200 

name	user	system	elapsed
FastqcData	0.083	0.000	0.112
FastqcDataList	0.528	0.000	0.615
TheoreticalGC-class	0.113	0.000	0.126
dot-FastqcFile-class	0.003	0.000	0.003
dot-addPercent	0.001	0.000	0.000
dot-emptyPlot	0.181	0.004	0.184
dot-makeDendro	0.480	0.000	0.481
dot-makeLabels	0.000	0.000	0.001
dot-splitByTab	0.004	0.000	0.003
estGcDistn	0.022	0.000	0.022
extract-methods	0.296	0.008	0.304
fqName-methods	0.404	0.004	0.409
fqcVersion	0.647	0.000	0.647
gcAvail	0.256	0.008	0.280
gcTheoretical	0.049	0.000	0.050
getColours-methods	0.002	0.000	0.002
getGC	0.008	0.008	0.017
getModule	0.373	0.004	0.376
getSummary	0.323	0.000	0.323
importNgsLogs	0.021	0.000	0.084
isCompressed	0.001	0.000	0.001
mData	0.016	0.000	0.017
maxAdapterContent	0.414	0.004	0.419
overRep2Fasta-methods	0.304	0.000	0.305
path	0.316	0.004	0.320
plotAdapterContent-methods	1.757	0.024	1.781
plotBaseQuals-methods	1.747	0.044	1.791
plotDupLevels-methods	0.956	0.020	0.976
plotGcContent-methods	0.653	0.004	0.657
plotKmers-methods	0.567	0.008	0.575
plotNContent-methods	0.372	0.000	0.372
plotOverrep-methods	0.595	0.000	0.595
plotReadTotals-methods	0.616	0.004	0.619
plotSeqContent-methods	0.552	0.004	0.556
plotSeqLengthDistn-methods	1.007	0.004	1.044
plotSeqQuals-methods	0.977	0.008	0.985
plotSummary-methods	0.514	0.004	0.519
pwf	0.004	0.000	0.003
readTotals	0.312	0.000	0.312
runFastQC-methods	0	0	0
writeHtmlReport	0	0	0