Multiple platform build/check report for BioC 3.9 - CHECK report for ngsReports on tokay2

Package: ngsReports

Version: 1.0.1

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ngsReports.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ngsReports_1.0.1.tar.gz

StartedAt: 2019-10-16 05:36:34 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 05:42:54 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 380.1 seconds

RetCode: 0

Status: OK

CheckDir: ngsReports.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ngsReports.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ngsReports_1.0.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/ngsReports.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/ngsReports_1.0.1.tar.gz && rm -rf ngsReports.buildbin-libdir && mkdir ngsReports.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ngsReports.buildbin-libdir ngsReports_1.0.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL ngsReports_1.0.1.zip && rm ngsReports_1.0.1.tar.gz ngsReports_1.0.1.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  627k  100  627k    0     0  9480k      0 --:--:-- --:--:-- --:--:-- 10.3M

install for i386

* 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
  converting help for package 'ngsReports'
    finding HTML links ... done
    FastqcData                              html  
    FastqcDataList                          html  
    PwfCols-class                           html  
    TheoreticalGC-class                     html  
    dot-FastqcFile-class                    html  
    dot-addPercent                          html  
    dot-emptyPlot                           html  
    dot-hidePWFRects                        html  
    dot-isValidBowtieLog                    html  
    dot-isValidDuplicationMetricsLog        html  
    dot-isValidHisat2Log                    html  
    dot-isValidStarLog                      html  
    dot-makeDendro                          html  
    dot-makeLabels                          html  
    dot-makeSidebar                         html  
    dot-parseBowtieLogs                     html  
    dot-parseDuplicationMetricsLogs         html  
    dot-parseHisat2Logs                     html  
    dot-parseStarLogs                       html  
    dot-renderDendro                        html  
    dot-scale_fill_pwf                      html  
    dot-splitByTab                          html  
    estGcDistn                              html  
    extract-methods                         html  
    fqName-methods                          html  
    fqcVersion                              html  
    gcAvail                                 html  
    gcTheoretical                           html  
    getColours-methods                      html  
    getGC                                   html  
    getModule                               html  
    getSummary                              html  
    importNgsLogs                           html  
    isCompressed                            html  
    mData                                   html  
    maxAdapterContent                       html  
    overRep2Fasta-methods                   html  
    path                                    html  
    plotAdapterContent-methods              html  
    plotBaseQuals-methods                   html  
    plotDupLevels-methods                   html  
    plotGcContent-methods                   html  
    plotKmers-methods                       html  
    plotNContent-methods                    html  
    plotOverrep-methods                     html  
    plotReadTotals-methods                  html  
    plotSeqContent-methods                  html  
    plotSeqLengthDistn-methods              html  
    plotSeqQuals-methods                    html  
    plotSummary-methods                     html  
    pwf                                     html  
    readTotals                              html  
    runFastQC-methods                       html  
    writeHtmlReport                         html  
** 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

install for x64

* installing *source* package 'ngsReports' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ngsReports' as ngsReports_1.0.1.zip
* DONE (ngsReports)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'ngsReports' successfully unpacked and MD5 sums checked


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 
  26.54    2.78   31.01


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 
  27.96    1.68   30.51

name	user	system	elapsed
FastqcData	0.14	0.00	0.29
FastqcDataList	0.52	0.03	1.66
TheoreticalGC-class	0.10	0.03	0.20
dot-FastqcFile-class	0.01	0.00	0.01
dot-addPercent	0	0	0
dot-emptyPlot	0.17	0.00	0.18
dot-makeDendro	0.55	0.00	0.54
dot-makeLabels	0	0	0
dot-splitByTab	0	0	0
estGcDistn	0.03	0.00	0.03
extract-methods	1.25	0.02	1.27
fqName-methods	0.28	0.02	0.29
fqcVersion	0.37	0.03	0.41
gcAvail	0.17	0.08	0.25
gcTheoretical	0.02	0.01	0.03
getColours-methods	0	0	0
getGC	0.02	0.02	0.03
getModule	0.25	0.15	0.41
getSummary	0.29	0.03	0.33
importNgsLogs	0.02	0.00	0.01
isCompressed	0.01	0.00	0.02
mData	0.02	0.00	0.01
maxAdapterContent	0.31	0.00	0.31
overRep2Fasta-methods	0.28	0.02	0.30
path	0.24	0.05	0.28
plotAdapterContent-methods	1.26	0.20	1.47
plotBaseQuals-methods	0.74	0.08	0.81
plotDupLevels-methods	0.87	0.01	0.89
plotGcContent-methods	0.57	0.05	0.61
plotKmers-methods	0.53	0.03	0.57
plotNContent-methods	0.32	0.02	0.34
plotOverrep-methods	0.47	0.00	0.46
plotReadTotals-methods	0.60	0.00	0.59
plotSeqContent-methods	0.40	0.01	0.43
plotSeqLengthDistn-methods	0.77	0.00	0.76
plotSeqQuals-methods	0.67	0.00	0.67
plotSummary-methods	0.42	0.03	0.46
pwf	0	0	0
readTotals	0.30	0.00	0.29
runFastQC-methods	0	0	0
writeHtmlReport	0	0	0

name	user	system	elapsed
FastqcData	0.13	0.00	0.12
FastqcDataList	0.47	0.05	0.52
TheoreticalGC-class	0.11	0.00	0.11
dot-FastqcFile-class	0	0	0
dot-addPercent	0	0	0
dot-emptyPlot	0.16	0.00	0.16
dot-makeDendro	0.50	0.02	0.51
dot-makeLabels	0	0	0
dot-splitByTab	0	0	0
estGcDistn	0.03	0.00	0.03
extract-methods	0.36	0.03	0.40
fqName-methods	0.29	0.00	0.29
fqcVersion	0.35	0.00	0.35
gcAvail	0.17	0.03	0.20
gcTheoretical	0.03	0.00	0.03
getColours-methods	0	0	0
getGC	0.00	0.01	0.02
getModule	0.33	0.00	0.32
getSummary	0.29	0.00	0.30
importNgsLogs	0.02	0.00	0.01
isCompressed	0	0	0
mData	0.01	0.00	0.02
maxAdapterContent	0.30	0.05	0.34
overRep2Fasta-methods	0.27	0.03	0.30
path	0.28	0.02	0.30
plotAdapterContent-methods	1.43	0.08	1.51
plotBaseQuals-methods	0.74	0.03	0.77
plotDupLevels-methods	1.03	0.03	1.06
plotGcContent-methods	0.91	0.03	0.94
plotKmers-methods	0.92	0.02	0.93
plotNContent-methods	0.62	0.00	0.63
plotOverrep-methods	0.86	0.01	0.87
plotReadTotals-methods	1.05	0.00	1.05
plotSeqContent-methods	0.55	0.03	0.58
plotSeqLengthDistn-methods	0.87	0.00	0.89
plotSeqQuals-methods	0.75	0.00	0.75
plotSummary-methods	0.47	0.00	0.47
pwf	0.00	0.02	0.01
readTotals	0.31	0.00	0.32
runFastQC-methods	0	0	0
writeHtmlReport	0	0	0

CHECK report for ngsReports on tokay2

Summary

Command output

Installation output

Tests output

Example timings