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CHECK report for twoddpcr on tokay1

This page was generated on 2021-05-06 12:34:05 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the twoddpcr package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1914/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
twoddpcr 1.14.0  (landing page)
Anthony Chiu
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/twoddpcr
Branch: RELEASE_3_12
Last Commit: c08b10c
Last Changed Date: 2020-10-27 11:21:51 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: twoddpcr
Version: 1.14.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:twoddpcr.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings twoddpcr_1.14.0.tar.gz
StartedAt: 2021-05-06 07:46:22 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 07:50:36 -0400 (Thu, 06 May 2021)
EllapsedTime: 254.2 seconds
RetCode: 0
Status:   OK   
CheckDir: twoddpcr.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:twoddpcr.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings twoddpcr_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/twoddpcr.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'twoddpcr/DESCRIPTION' ... OK
* this is package 'twoddpcr' version '1.14.0'
* 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 'twoddpcr' 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
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
ggplot.well  8.62   0.22    8.85
knnClassify  7.97   0.03    8.00
flatPlot     6.12   0.18    6.31
gridClassify 5.73   0.08    5.82
dropletPlot  5.28   0.12    5.41
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
knnClassify  8.44   0.05    8.49
ggplot.well  7.98   0.18    8.17
gridClassify 7.11   0.13    7.23
flatPlot     5.28   0.16    5.43
* 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

twoddpcr.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/twoddpcr_1.14.0.tar.gz && rm -rf twoddpcr.buildbin-libdir && mkdir twoddpcr.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=twoddpcr.buildbin-libdir twoddpcr_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL twoddpcr_1.14.0.zip && rm twoddpcr_1.14.0.tar.gz twoddpcr_1.14.0.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
100  875k  100  875k    0     0  33.6M      0 --:--:-- --:--:-- --:--:-- 35.6M

install for i386

* installing *source* package 'twoddpcr' ...
** 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 'twoddpcr'
    finding HTML links ... done
    KRAScounts                              html  
    KRASdata                                html  
    amplitudes                              html  
    basicsSummary                           html  
    castSummary                             html  
    classCov                                html  
    classMeans                              html  
    classStats                              html  
    clusterCentres                          html  
    copiesSummary                           html  
    ddpcr                                   html  
    ddpcrPlate-class                        html  
    ddpcrWell-class                         html  
    ddpcrWell-methods                       html  
    dot-classifyDfOnChannel                 html  
    dot-classifyOnChannel                   html  
    dot-classwiseMahalanobisRain            html  
    dot-cov                                 html  
    dot-dependentCols                       html  
    dot-essentialDependentCols              html  
    dot-extractWellNames                    html  
    dot-getAllSummary                       html  
    dot-getChannelCentres                   html  
    dot-getClassificationData               html  
    dot-getMutCopies                        html  
    dot-getWellNames                        html  
    dot-getWtCopies                         html  
    dot-isTwoDimDataFrame                   html  
    dot-isWideForm                          html  
    dot-mahDist                             html  
    dot-matrixInverse                       html  
    dot-numberOfWells                       html  
    dot-renormaliseByChannel                html  
    dot-renormaliseWell                     html  
    dot-roundIt                             html  
    dot-slice                               html  
    dot-totalCopies                         html  
    drawBlank                               html  
    dropletPlot                             html  
    elementType-SimpleList-method           html  
    exportTable                             html  
    extractPlateName                        html  
    extractWellNames                        html  
    facetPlot                               html  
    flatPlot                                html  
    fullCopiesSummary                       html  
    fullCountsSummary                       html  
    getCutOff                               html  
    ggplot.well                             html  
    gridClassify                            html  
    heatPlot                                html  
    kmeansClassify                          html  
    knnClassify                             html  
    mahalanobisRain                         html  
    mutantCopiesSummary                     html  
    numDroplets                             html  
    numericInputRow                         html  
    parseClusterCounts                      html  
    plateClassification                     html  
    plateClassificationMethod               html  
    plateSummary                            html  
    positiveCounts                          html  
    readCSVDataFrame                        html  
    relabelClasses                          html  
    removeDropletClasses                    html  
    renormalisePlate                        html  
    sdRain                                  html  
    setChannelNames                         html  
    setDropletVolume                        html  
    shinyVis                                html  
    shinyVisApp                             html  
    shinyVisServer                          html  
    shinyVisUI                              html  
    sortDataFrame                           html  
    sortWells                               html  
    textInputRow                            html  
    thresholdClassify                       html  
    twoddpcr-package                        html  
    wellClassification                      html  
    wellClassificationMethod                html  
    whiteTheme                              html  
    wildTypeCopiesSummary                   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 'twoddpcr' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'twoddpcr' as twoddpcr_1.14.0.zip
* DONE (twoddpcr)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'twoddpcr' successfully unpacked and MD5 sums checked

Tests output

twoddpcr.Rcheck/tests_i386/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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(twoddpcr)
> 
> test_check("twoddpcr")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 156 ]
> 
> proc.time()
   user  system elapsed 
  11.23    0.34   11.59 

twoddpcr.Rcheck/tests_x64/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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(twoddpcr)
> 
> test_check("twoddpcr")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 156 ]
> 
> proc.time()
   user  system elapsed 
   9.64    0.32   10.04 

Example timings

twoddpcr.Rcheck/examples_i386/twoddpcr-Ex.timings

nameusersystemelapsed
amplitudes0.920.050.97
basicsSummary0.010.000.01
castSummary0.030.000.03
classCov0.080.000.08
classMeans0.090.000.09
classStats0.110.000.11
clusterCentres1.890.001.89
copiesSummary0.020.000.02
ddpcrPlate-class0.810.000.81
ddpcrWell-class0.050.000.05
ddpcrWell-methods0.470.000.46
dropletPlot5.280.125.41
exportTable0.140.000.20
extractPlateName000
extractWellNames000
facetPlot2.640.042.68
flatPlot6.120.186.31
fullCopiesSummary0.020.000.01
fullCountsSummary0.030.000.03
ggplot.well8.620.228.85
gridClassify5.730.085.82
heatPlot1.540.051.57
kmeansClassify1.200.031.24
knnClassify7.970.038.00
mahalanobisRain0.690.000.69
mutantCopiesSummary0.010.000.01
numDroplets0.440.020.46
parseClusterCounts0.010.000.01
plateClassification1.570.001.56
plateClassificationMethod0.680.000.69
plateSummary2.50.02.5
positiveCounts0.050.000.05
readCSVDataFrame0.000.010.01
relabelClasses0.130.000.13
removeDropletClasses1.140.031.18
renormalisePlate3.780.063.84
sdRain3.610.003.61
setChannelNames0.020.000.01
setDropletVolume000
sortDataFrame000
sortWells0.550.000.55
thresholdClassify2.420.002.42
wellClassification0.030.000.03
wellClassificationMethod0.030.000.04
whiteTheme1.670.021.69
wildTypeCopiesSummary000

twoddpcr.Rcheck/examples_x64/twoddpcr-Ex.timings

nameusersystemelapsed
amplitudes0.480.030.51
basicsSummary0.020.000.02
castSummary0.030.000.03
classCov0.050.000.05
classMeans0.040.000.04
classStats0.070.010.08
clusterCentres1.030.001.03
copiesSummary0.010.000.02
ddpcrPlate-class0.460.000.45
ddpcrWell-class0.040.000.05
ddpcrWell-methods0.570.000.56
dropletPlot4.500.054.55
exportTable0.110.050.17
extractPlateName000
extractWellNames000
facetPlot2.250.042.30
flatPlot5.280.165.43
fullCopiesSummary0.010.000.02
fullCountsSummary0.020.020.03
ggplot.well7.980.188.17
gridClassify7.110.137.23
heatPlot1.760.051.82
kmeansClassify1.520.091.60
knnClassify8.440.058.49
mahalanobisRain0.970.010.98
mutantCopiesSummary000
numDroplets0.430.000.44
parseClusterCounts0.020.000.02
plateClassification1.480.001.48
plateClassificationMethod0.570.000.56
plateSummary2.400.002.41
positiveCounts0.020.000.02
readCSVDataFrame000
relabelClasses0.040.000.05
removeDropletClasses0.790.000.78
renormalisePlate3.950.003.96
sdRain4.090.004.09
setChannelNames000
setDropletVolume000
sortDataFrame000
sortWells0.660.000.66
thresholdClassify2.840.022.86
wellClassification0.030.000.03
wellClassificationMethod0.040.000.03
whiteTheme1.820.031.86
wildTypeCopiesSummary0.020.000.01