Multiple platform build/check report for BioC 3.10 - CHECK report for ngsReports on malbec1

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:ngsReports.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings ngsReports_1.2.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/ngsReports.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.2.0’
* 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

Installation output

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL ngsReports
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* installing to library ‘/home/biocbuild/bbs-3.10-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)

Tests output


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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: 205 | SKIPPED: 0 | WARNINGS: 5 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 39.116   1.156  38.184

Example timings

name	user	system	elapsed
FastqcData	0.120	0.000	0.145
FastqcDataList	0.572	0.016	0.689
TheoreticalGC-class	0.160	0.004	0.192
dot-FastqcFile-class	0.004	0.000	0.002
dot-addPercent	0	0	0
dot-emptyPlot	0.112	0.000	0.113
dot-makeDendro	0.576	0.008	0.585
dot-makeLabels	0.004	0.000	0.002
dot-splitByTab	0.004	0.000	0.006
estGcDistn	0.028	0.000	0.025
extract-methods	1.080	0.008	1.092
fqName-methods	0.552	0.012	0.578
fqcVersion	0.576	0.036	0.626
gcAvail	0.264	0.052	0.317
gcTheoretical	0.044	0.008	0.053
getColours-methods	0.004	0.000	0.003
getGC	0.020	0.000	0.022
getModule	0.660	0.012	0.676
getSummary	0.580	0.004	0.587
importNgsLogs	0.036	0.000	0.047
isCompressed	0.000	0.000	0.002
mData	0.024	0.000	0.024
maxAdapterContent	0.640	0.004	0.648
overRep2Fasta-methods	0.520	0.000	0.521
path	0.380	0.000	0.383
plotAdapterContent-methods	1.872	0.040	1.912
plotAlignmentSummary	0.472	0.008	0.629
plotAssemblyStats	1.032	0.004	1.056
plotBaseQuals-methods	1.336	0.000	1.344
plotDupLevels-methods	1.108	0.012	1.131
plotFastqcPCA-methods	1.200	0.004	1.205
plotGcContent-methods	0.832	0.008	0.839
plotKmers-methods	0.608	0.008	0.619
plotNContent-methods	0.664	0.000	0.668
plotOverrep-methods	0.952	0.008	0.961
plotReadTotals-methods	1.088	0.000	1.090
plotSeqContent-methods	0.700	0.012	0.711
plotSeqLengthDistn-methods	1.188	0.000	1.191
plotSeqQuals-methods	1.276	0.008	1.284
plotSummary-methods	0.880	0.004	0.881
pwf	0.004	0.000	0.006
readTotals	0.572	0.004	0.588
runFastQC-methods	0.000	0.000	0.001
writeHtmlReport	0.004	0.000	0.001

CHECK report for ngsReports on malbec1

Summary

Command output

Installation output

Tests output

Example timings