Multiple platform build/check report for BioC 3.11 - CHECK report for ngsReports on celaya2

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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_1.3.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/ngsReports.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.3.0’
* 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

Installation output

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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/4.0/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)

Tests output


R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
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: 205 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 50.572   5.164  53.554

Example timings

name	user	system	elapsed
FastqcData	0.149	0.015	0.171
FastqcDataList	0.555	0.026	0.591
TheoreticalGC-class	0.146	0.004	0.150
dot-FastqcFile-class	0.003	0.001	0.003
dot-addPercent	0.000	0.001	0.001
dot-emptyPlot	0.196	0.014	0.210
dot-makeDendro	1.507	0.028	1.535
dot-makeLabels	0.001	0.001	0.002
dot-splitByTab	0.007	0.001	0.009
estGcDistn	0.046	0.002	0.049
extract-methods	0.642	0.031	0.674
fqName-methods	0.656	0.036	0.691
fqcVersion	0.922	0.120	1.042
gcAvail	0.041	0.008	0.050
gcTheoretical	0.070	0.012	0.082
getColours-methods	0.004	0.001	0.005
getGC	0.033	0.006	0.039
getModule	0.638	0.031	0.669
getSummary	0.613	0.017	0.630
importNgsLogs	0.045	0.001	0.047
isCompressed	0.003	0.002	0.005
mData	0.036	0.001	0.037
maxAdapterContent	0.706	0.018	0.723
overRep2Fasta-methods	0.656	0.025	0.682
path	0.676	0.018	0.694
plotAdapterContent-methods	2.677	0.180	2.859
plotAlignmentSummary	0.555	0.008	0.564
plotAssemblyStats	1.004	0.015	1.020
plotBaseQuals-methods	1.505	0.032	1.540
plotDupLevels-methods	1.739	0.029	1.768
plotFastqcPCA-methods	1.359	0.028	1.389
plotGcContent-methods	1.215	0.033	1.249
plotKmers-methods	1.068	0.019	1.088
plotNContent-methods	0.763	0.020	0.784
plotOverrep-methods	1.208	0.019	1.228
plotReadTotals-methods	1.111	0.015	1.126
plotSeqContent-methods	0.943	0.026	0.969
plotSeqLengthDistn-methods	1.511	0.029	1.546
plotSeqQuals-methods	1.413	0.022	1.436
plotSummary-methods	0.935	0.019	0.955
pwf	0.005	0.001	0.007
readTotals	0.549	0.018	0.567
runFastQC-methods	0.001	0.000	0.000
writeHtmlReport	0.000	0.000	0.001

CHECK report for ngsReports on celaya2

Summary

Command output

Installation output

Tests output

Example timings