Multiple platform build/check report for BioC 3.13 - CHECK results for ngsReports on tokay2

Package: ngsReports

Version: 1.8.1

Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ngsReports.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ngsReports_1.8.1.tar.gz

StartedAt: 2021-10-15 02:44:54 -0400 (Fri, 15 Oct 2021)

EndedAt: 2021-10-15 02:48:53 -0400 (Fri, 15 Oct 2021)

EllapsedTime: 238.9 seconds

RetCode: 0

Status: OK

CheckDir: ngsReports.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ngsReports.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ngsReports_1.8.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/ngsReports.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.8.1'
* 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 LazyData ... 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 http://155.52.207.165/BBS/3.13/bioc/src/contrib/ngsReports_1.8.1.tar.gz && rm -rf ngsReports.buildbin-libdir && mkdir ngsReports.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ngsReports.buildbin-libdir ngsReports_1.8.1.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL ngsReports_1.8.1.zip && rm ngsReports_1.8.1.tar.gz ngsReports_1.8.1.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
  0  657k    0  2487    0     0  30216      0  0:00:22 --:--:--  0:00:22 30329
100  657k  100  657k    0     0  1338k      0 --:--:-- --:--:-- --:--:-- 1338k

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-isValidMacs2CallpeakLog             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-parseMacs2CallpeakLogs              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  
    importSJ                                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  
*** copying figures
** 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_1.8.1.zip
* DONE (ngsReports)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'ngsReports' successfully unpacked and MD5 sums checked


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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.max, which.min

Loading required package: ggplot2
Loading required package: tibble
> 
> test_check("ngsReports")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 201 ]
> 
> proc.time()
   user  system elapsed 
  18.45    1.87   21.20


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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.max, which.min

Loading required package: ggplot2
Loading required package: tibble
> 
> test_check("ngsReports")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 201 ]
> 
> proc.time()
   user  system elapsed 
  19.09    1.31   21.18

name	user	system	elapsed
FastqcData	0.16	0.02	0.39
FastqcDataList	0.56	0.00	0.69
TheoreticalGC-class	0.10	0.00	0.28
dot-FastqcFile-class	0	0	0
dot-addPercent	0	0	0
dot-emptyPlot	0.47	0.00	0.47
dot-makeDendro	0.39	0.00	0.39
dot-makeLabels	0	0	0
dot-splitByTab	0.01	0.00	0.01
estGcDistn	0.03	0.00	0.03
extract-methods	0.44	0.08	0.52
fqName-methods	0.50	0.04	0.55
fqcVersion	0.36	0.15	0.50
gcAvail	0.02	0.00	0.01
gcTheoretical	0.04	0.00	0.05
getColours-methods	0	0	0
getGC	0.02	0.00	0.01
getModule	0.39	0.00	0.39
getSummary	0.33	0.00	0.33
importNgsLogs	0.01	0.00	0.02
importSJ	0.01	0.00	0.02
isCompressed	0.00	0.01	0.02
mData	0.02	0.00	0.01
maxAdapterContent	0.37	0.02	0.42
overRep2Fasta-methods	0.44	0.00	0.56
path	0.31	0.00	0.31
plotAdapterContent-methods	1.25	0.01	1.27
plotAlignmentSummary	0.21	0.00	0.20
plotAssemblyStats	0.42	0.00	0.42
plotBaseQuals-methods	0.62	0.02	0.64
plotDupLevels-methods	0.77	0.00	0.77
plotFastqcPCA-methods	0.42	0.00	0.42
plotGcContent-methods	0.47	0.09	0.56
plotKmers-methods	0.44	0.03	0.47
plotNContent-methods	0.31	0.02	0.33
plotOverrep-methods	0.45	0.01	0.47
plotReadTotals-methods	0.54	0.02	0.55
plotSeqContent-methods	0.40	0.02	0.42
plotSeqLengthDistn-methods	0.74	0.00	0.73
plotSeqQuals-methods	0.65	0.00	0.66
plotSummary-methods	0.42	0.00	0.42
pwf	0	0	0
readTotals	0.24	0.05	0.28
writeHtmlReport	0	0	0

name	user	system	elapsed
FastqcData	0.07	0.00	0.06
FastqcDataList	0.39	0.00	0.39
TheoreticalGC-class	0.05	0.02	0.06
dot-FastqcFile-class	0.00	0.01	0.02
dot-addPercent	0	0	0
dot-emptyPlot	0.52	0.00	0.68
dot-makeDendro	0.29	0.02	0.32
dot-makeLabels	0	0	0
dot-splitByTab	0	0	0
estGcDistn	0.02	0.00	0.01
extract-methods	0.26	0.01	0.28
fqName-methods	0.25	0.03	0.28
fqcVersion	0.36	0.00	0.36
gcAvail	0.01	0.00	0.02
gcTheoretical	0.04	0.00	0.03
getColours-methods	0	0	0
getGC	0.01	0.00	0.02
getModule	0.31	0.00	0.31
getSummary	0.27	0.03	0.30
importNgsLogs	0.01	0.00	0.01
importSJ	0.05	0.00	0.05
isCompressed	0	0	0
mData	0.02	0.00	0.01
maxAdapterContent	0.31	0.02	0.33
overRep2Fasta-methods	0.28	0.03	0.32
path	0.28	0.00	0.28
plotAdapterContent-methods	1.36	0.03	1.39
plotAlignmentSummary	0.24	0.00	0.23
plotAssemblyStats	0.48	0.02	0.50
plotBaseQuals-methods	0.72	0.00	0.72
plotDupLevels-methods	0.83	0.01	0.84
plotFastqcPCA-methods	0.45	0.00	0.46
plotGcContent-methods	0.56	0.03	0.59
plotKmers-methods	0.55	0.00	0.55
plotNContent-methods	0.33	0.02	0.34
plotOverrep-methods	0.47	0.01	0.49
plotReadTotals-methods	0.56	0.02	0.57
plotSeqContent-methods	0.44	0.00	0.44
plotSeqLengthDistn-methods	0.95	0.00	1.17
plotSeqQuals-methods	0.87	0.00	0.88
plotSummary-methods	0.52	0.00	0.51
pwf	0.02	0.00	0.02
readTotals	0.36	0.00	0.36
writeHtmlReport	0	0	0

CHECK results for ngsReports on tokay2

Summary

Command output

Installation output

Tests output

Example timings