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This page was generated on 2022-01-17 13:06:41 -0500 (Mon, 17 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for ngsReports on tokay2


To the developers/maintainers of the ngsReports package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ngsReports.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1295/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ngsReports 1.10.0  (landing page)
Steve Pederson
Snapshot Date: 2022-01-16 01:55:05 -0500 (Sun, 16 Jan 2022)
git_url: https://git.bioconductor.org/packages/ngsReports
git_branch: RELEASE_3_14
git_last_commit: b18d9df
git_last_commit_date: 2021-10-26 12:50:47 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ngsReports
Version: 1.10.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ngsReports.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ngsReports_1.10.0.tar.gz
StartedAt: 2022-01-17 00:43:15 -0500 (Mon, 17 Jan 2022)
EndedAt: 2022-01-17 00:47:08 -0500 (Mon, 17 Jan 2022)
EllapsedTime: 232.8 seconds
RetCode: 0
Status:   OK  
CheckDir: ngsReports.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ngsReports.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ngsReports_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/ngsReports.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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 '1.10.0'
* 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 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


Installation output

ngsReports.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/ngsReports_1.10.0.tar.gz && rm -rf ngsReports.buildbin-libdir && mkdir ngsReports.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ngsReports.buildbin-libdir ngsReports_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL ngsReports_1.10.0.zip && rm ngsReports_1.10.0.tar.gz ngsReports_1.10.0.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
 15  660k   15  102k    0     0   780k      0 --:--:-- --:--:-- --:--:--  779k
100  660k  100  660k    0     0  2811k      0 --:--:-- --:--:-- --:--:-- 2810k

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_1.10.0.zip
* DONE (ngsReports)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'ngsReports' successfully unpacked and MD5 sums checked

Tests output

ngsReports.Rcheck/tests_i386/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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

Attaching package: 'BiocGenerics'

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 0 | SKIP 0 | PASS 205 ]
> 
> proc.time()
   user  system elapsed 
  19.92    1.82   23.23 

ngsReports.Rcheck/tests_x64/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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

Attaching package: 'BiocGenerics'

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 0 | SKIP 0 | PASS 205 ]
> 
> proc.time()
   user  system elapsed 
  17.39    1.43   19.59 

Example timings

ngsReports.Rcheck/examples_i386/ngsReports-Ex.timings

nameusersystemelapsed
FastqcData0.150.000.28
FastqcDataList0.580.010.80
TheoreticalGC-class0.140.000.17
dot-FastqcFile-class000
dot-addPercent000
dot-emptyPlot0.520.000.52
dot-makeDendro0.360.020.37
dot-makeLabels000
dot-splitByTab0.010.000.02
estGcDistn0.020.000.02
extract-methods0.280.050.32
fqName-methods0.260.090.36
fqcVersion0.440.020.46
gcAvail0.030.000.03
gcTheoretical0.030.010.04
getColours-methods000
getGC0.040.000.04
getModule0.420.000.42
getSummary0.420.000.42
importNgsLogs0.010.000.01
importSJ0.020.000.02
isCompressed000
mData0.010.000.02
maxAdapterContent0.350.010.36
overRep2Fasta-methods0.310.020.32
path0.290.010.32
plotAdapterContent-methods1.330.021.34
plotAlignmentSummary0.220.000.22
plotAssemblyStats0.450.000.45
plotBaseQuals-methods0.680.000.67
plotDupLevels-methods0.810.000.82
plotFastqcPCA-methods0.420.030.45
plotGcContent-methods0.630.050.67
plotKmers-methods0.500.030.53
plotNContent-methods0.340.010.36
plotOverrep-methods0.50.00.5
plotReadTotals-methods0.550.020.57
plotSeqContent-methods0.400.030.43
plotSeqLengthDistn-methods0.770.020.78
plotSeqQuals-methods0.650.010.68
plotSummary-methods0.430.030.45
pwf000
readTotals0.310.020.33
writeHtmlReport000

ngsReports.Rcheck/examples_x64/ngsReports-Ex.timings

nameusersystemelapsed
FastqcData0.060.000.06
FastqcDataList0.360.020.38
TheoreticalGC-class0.060.000.07
dot-FastqcFile-class000
dot-addPercent000
dot-emptyPlot0.400.000.41
dot-makeDendro0.290.010.29
dot-makeLabels000
dot-splitByTab000
estGcDistn0.030.000.04
extract-methods0.250.020.26
fqName-methods0.230.050.28
fqcVersion0.340.010.36
gcAvail0.040.000.03
gcTheoretical0.030.000.03
getColours-methods000
getGC0.030.000.04
getModule0.450.030.48
getSummary0.310.030.34
importNgsLogs0.030.000.03
importSJ0.030.000.03
isCompressed0.000.020.02
mData0.020.000.01
maxAdapterContent0.330.020.35
overRep2Fasta-methods0.280.030.31
path0.290.000.30
plotAdapterContent-methods1.320.021.33
plotAlignmentSummary0.220.000.22
plotAssemblyStats0.50.00.5
plotBaseQuals-methods0.70.00.7
plotDupLevels-methods0.840.000.85
plotFastqcPCA-methods0.440.010.45
plotGcContent-methods0.590.020.61
plotKmers-methods0.500.010.51
plotNContent-methods0.330.020.35
plotOverrep-methods0.470.000.47
plotReadTotals-methods0.560.000.56
plotSeqContent-methods0.420.000.42
plotSeqLengthDistn-methods0.820.020.83
plotSeqQuals-methods0.730.010.75
plotSummary-methods0.470.000.47
pwf000
readTotals0.280.000.28
writeHtmlReport000