Multiple platform build/check report for BioC 3.10 - CHECK report for ngsReports on tokay1

Package: ngsReports

Version: 1.2.0

Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ngsReports.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings ngsReports_1.2.0.tar.gz

StartedAt: 2020-04-15 05:07:55 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 05:14:35 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 399.3 seconds

RetCode: 0

Status: OK

CheckDir: ngsReports.Rcheck

Warnings: 0

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

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/ngsReports_1.2.0.tar.gz && rm -rf ngsReports.buildbin-libdir && mkdir ngsReports.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ngsReports.buildbin-libdir ngsReports_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL ngsReports_1.2.0.zip && rm ngsReports_1.2.0.tar.gz ngsReports_1.2.0.zip
###
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  % 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  651k  100  651k    0     0  4601k      0 --:--:-- --:--:-- --:--:-- 4753k

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-getToolName                         html  
    dot-hidePWFRects                        html  
    dot-isValidAdapterRemovalLog            html  
    dot-isValidBowtieLog                    html  
    dot-isValidBuscoLog                     html  
    dot-isValidCutadaptLog                  html  
    dot-isValidDuplicationMetricsLog        html  
    dot-isValidFeatureCountsLog             html  
    dot-isValidFlagstatLog                  html  
    dot-isValidHisat2Log                    html  
    dot-isValidQuastLog                     html  
    dot-isValidStarLog                      html  
    dot-isValidTrimmomaticLog               html  
    dot-makeDendro                          html  
    dot-makeLabels                          html  
    dot-makeSidebar                         html  
    dot-parseAdapterRemovalLogs             html  
    dot-parseBowtieLogs                     html  
    dot-parseBuscoLogs                      html  
    dot-parseCutadaptLogs                   html  
    dot-parseDuplicationMetricsLogs         html  
    dot-parseFeatureCountsLogs              html  
    dot-parseFlagstatLogs                   html  
    dot-parseHisat2Logs                     html  
    dot-parseQuastLogs                      html  
    dot-parseStarLogs                       html  
    dot-parseTrimmomaticLogs                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  
    plotAlignmentSummary                    html  
    plotAssemblyStats                       html  
    plotBaseQuals-methods                   html  
    plotDupLevels-methods                   html  
    plotFastqcPCA-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_1.2.0.zip
* DONE (ngsReports)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'ngsReports' successfully unpacked and MD5 sums checked


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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: 205 | SKIPPED: 0 | WARNINGS: 5 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  31.62    2.85   35.65


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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: 205 | SKIPPED: 0 | WARNINGS: 5 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  33.56    1.87   36.37

name	user	system	elapsed
FastqcData	0.12	0.00	0.18
FastqcDataList	0.27	0.11	0.53
TheoreticalGC-class	0.11	0.02	0.16
dot-FastqcFile-class	0.02	0.00	0.01
dot-addPercent	0	0	0
dot-emptyPlot	0.22	0.01	0.24
dot-makeDendro	0.46	0.17	0.64
dot-makeLabels	0	0	0
dot-splitByTab	0	0	0
estGcDistn	0.05	0.00	0.05
extract-methods	0.58	0.00	0.59
fqName-methods	0.50	0.01	0.52
fqcVersion	0.52	0.02	0.54
gcAvail	0.27	0.00	0.26
gcTheoretical	0.04	0.00	0.05
getColours-methods	0	0	0
getGC	0.03	0.00	0.03
getModule	0.39	0.08	0.47
getSummary	0.35	0.00	0.34
importNgsLogs	0.03	0.00	0.03
isCompressed	0	0	0
mData	0.03	0.00	0.03
maxAdapterContent	0.50	0.03	0.54
overRep2Fasta-methods	0.28	0.06	0.34
path	0.35	0.00	0.34
plotAdapterContent-methods	1.54	0.28	1.83
plotAlignmentSummary	0.27	0.00	0.27
plotAssemblyStats	0.64	0.13	0.76
plotBaseQuals-methods	0.76	0.14	0.91
plotDupLevels-methods	0.96	0.08	1.03
plotFastqcPCA-methods	0.69	0.01	0.70
plotGcContent-methods	0.70	0.00	0.71
plotKmers-methods	0.61	0.03	0.64
plotNContent-methods	0.39	0.00	0.39
plotOverrep-methods	0.69	0.05	0.73
plotReadTotals-methods	1.03	0.05	1.08
plotSeqContent-methods	0.93	0.03	0.95
plotSeqLengthDistn-methods	1.29	0.00	1.30
plotSeqQuals-methods	1.07	0.03	1.09
plotSummary-methods	0.62	0.00	0.63
pwf	0	0	0
readTotals	0.33	0.03	0.35
runFastQC-methods	0	0	0
writeHtmlReport	0	0	0

name	user	system	elapsed
FastqcData	0.08	0.00	0.07
FastqcDataList	0.29	0.00	0.30
TheoreticalGC-class	0.08	0.00	0.08
dot-FastqcFile-class	0	0	0
dot-addPercent	0	0	0
dot-emptyPlot	0.14	0.00	0.14
dot-makeDendro	0.31	0.00	0.31
dot-makeLabels	0	0	0
dot-splitByTab	0	0	0
estGcDistn	0.02	0.00	0.01
extract-methods	0.30	0.01	0.31
fqName-methods	0.28	0.02	0.30
fqcVersion	0.39	0.02	0.41
gcAvail	0.19	0.00	0.18
gcTheoretical	0.03	0.00	0.03
getColours-methods	0	0	0
getGC	0.01	0.00	0.02
getModule	0.30	0.03	0.33
getSummary	0.94	0.04	0.98
importNgsLogs	0.01	0.00	0.02
isCompressed	0	0	0
mData	0.02	0.00	0.01
maxAdapterContent	0.33	0.02	0.35
overRep2Fasta-methods	0.26	0.03	0.29
path	0.36	0.00	0.36
plotAdapterContent-methods	1.66	0.02	1.68
plotAlignmentSummary	0.28	0.00	0.28
plotAssemblyStats	0.7	0.0	0.7
plotBaseQuals-methods	0.79	0.01	0.80
plotDupLevels-methods	1	0	1
plotFastqcPCA-methods	0.64	0.02	0.65
plotGcContent-methods	0.67	0.01	0.69
plotKmers-methods	0.56	0.02	0.58
plotNContent-methods	0.36	0.00	0.36
plotOverrep-methods	0.55	0.00	0.54
plotReadTotals-methods	0.64	0.00	0.65
plotSeqContent-methods	0.40	0.05	0.45
plotSeqLengthDistn-methods	0.94	0.00	0.94
plotSeqQuals-methods	0.80	0.02	0.81
plotSummary-methods	0.50	0.01	0.52
pwf	0.01	0.00	0.02
readTotals	0.32	0.02	0.32
runFastQC-methods	0	0	0
writeHtmlReport	0	0	0

CHECK report for ngsReports on tokay1

Summary

Command output

Installation output

Tests output

Example timings