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CHECK report for ngsReports on tokay2

This page was generated on 2020-10-17 11:57:16 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE ngsReports PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1195/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ngsReports 1.4.2
Steve Pederson
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/ngsReports
Branch: RELEASE_3_11
Last Commit: 530ae1b
Last Changed Date: 2020-06-08 12:27:17 -0400 (Mon, 08 Jun 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ngsReports
Version: 1.4.2
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ngsReports.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings ngsReports_1.4.2.tar.gz
StartedAt: 2020-10-17 06:29:26 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 06:36:54 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 448.0 seconds
RetCode: 0
Status:  OK  
CheckDir: ngsReports.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ngsReports.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings ngsReports_1.4.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/ngsReports.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.4.2'
* 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


Installation output

ngsReports.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/ngsReports_1.4.2.tar.gz && rm -rf ngsReports.buildbin-libdir && mkdir ngsReports.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ngsReports.buildbin-libdir ngsReports_1.4.2.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL ngsReports_1.4.2.zip && rm ngsReports_1.4.2.tar.gz ngsReports_1.4.2.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  657k  100  657k    0     0   9.7M      0 --:--:-- --:--:-- --:--:-- 11.0M

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_1.4.2.zip
* DONE (ngsReports)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'ngsReports' successfully unpacked and MD5 sums checked

Tests output

ngsReports.Rcheck/tests_i386/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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: 202 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  33.82    3.20   37.76 

ngsReports.Rcheck/tests_x64/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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: 202 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  32.26    1.53   34.60 

Example timings

ngsReports.Rcheck/examples_i386/ngsReports-Ex.timings

nameusersystemelapsed
FastqcData0.080.000.08
FastqcDataList0.250.110.36
TheoreticalGC-class0.080.010.09
dot-FastqcFile-class0.010.000.02
dot-addPercent000
dot-emptyPlot0.080.070.14
dot-makeDendro0.350.070.42
dot-makeLabels000
dot-splitByTab000
estGcDistn0.010.000.01
extract-methods0.350.000.35
fqName-methods0.290.020.31
fqcVersion0.410.030.44
gcAvail0.010.000.01
gcTheoretical0.040.000.04
getColours-methods000
getGC0.010.000.01
getModule0.350.000.34
getSummary0.320.020.35
importNgsLogs0.020.000.01
isCompressed0.010.000.02
mData000
maxAdapterContent0.380.030.40
overRep2Fasta-methods0.340.030.38
path0.330.000.32
plotAdapterContent-methods1.330.421.75
plotAlignmentSummary0.300.080.38
plotAssemblyStats0.480.050.53
plotBaseQuals-methods0.710.040.75
plotDupLevels-methods0.840.020.86
plotFastqcPCA-methods0.660.000.65
plotGcContent-methods0.820.030.86
plotKmers-methods1.030.001.03
plotNContent-methods0.610.010.63
plotOverrep-methods0.580.020.59
plotReadTotals-methods0.660.000.66
plotSeqContent-methods0.530.030.56
plotSeqLengthDistn-methods0.920.000.92
plotSeqQuals-methods0.70.00.7
plotSummary-methods0.450.020.47
pwf0.020.000.02
readTotals0.330.000.32
runFastQC-methods000
writeHtmlReport000

ngsReports.Rcheck/examples_x64/ngsReports-Ex.timings

nameusersystemelapsed
FastqcData0.140.000.14
FastqcDataList0.540.000.54
TheoreticalGC-class0.250.000.25
dot-FastqcFile-class000
dot-addPercent000
dot-emptyPlot0.170.000.17
dot-makeDendro0.550.000.55
dot-makeLabels0.010.000.01
dot-splitByTab000
estGcDistn0.050.000.05
extract-methods1.470.031.50
fqName-methods0.500.020.52
fqcVersion0.670.030.71
gcAvail0.030.000.04
gcTheoretical0.060.000.06
getColours-methods000
getGC0.040.000.03
getModule0.570.050.62
getSummary0.580.010.60
importNgsLogs0.050.000.04
isCompressed000
mData0.030.000.04
maxAdapterContent0.580.030.61
overRep2Fasta-methods0.610.030.64
path0.530.020.55
plotAdapterContent-methods2.540.112.64
plotAlignmentSummary0.420.010.44
plotAssemblyStats0.680.000.68
plotBaseQuals-methods0.740.020.75
plotDupLevels-methods1.190.031.22
plotFastqcPCA-methods0.650.000.66
plotGcContent-methods0.640.000.64
plotKmers-methods0.520.020.53
plotNContent-methods0.420.010.44
plotOverrep-methods0.590.020.61
plotReadTotals-methods0.610.030.64
plotSeqContent-methods0.490.050.53
plotSeqLengthDistn-methods1.140.011.17
plotSeqQuals-methods0.780.000.78
plotSummary-methods0.450.000.46
pwf0.020.000.01
readTotals0.390.000.39
runFastQC-methods000
writeHtmlReport000