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CHECK report for twoddpcr on merida1

This page was generated on 2021-05-06 12:37:18 -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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:twoddpcr.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings twoddpcr_1.14.0.tar.gz
StartedAt: 2021-05-06 07:07:31 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 07:10:00 -0400 (Thu, 06 May 2021)
EllapsedTime: 149.1 seconds
RetCode: 0
Status:   OK  
CheckDir: twoddpcr.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:twoddpcr.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings twoddpcr_1.14.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/twoddpcr.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... 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
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
knnClassify  8.135  0.159   8.309
ggplot.well  6.430  0.219   6.664
gridClassify 5.320  0.123   5.455
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL twoddpcr
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* 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
** 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
* DONE (twoddpcr)

Tests output

twoddpcr.Rcheck/tests/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-apple-darwin17.0 (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 
 10.495   0.508  10.997 

Example timings

twoddpcr.Rcheck/twoddpcr-Ex.timings

nameusersystemelapsed
amplitudes0.4550.0270.481
basicsSummary0.0080.0010.009
castSummary0.0370.0060.044
classCov0.0690.0090.079
classMeans0.0940.0150.109
classStats0.1010.0140.116
clusterCentres1.0260.0641.092
copiesSummary0.0060.0010.008
ddpcrPlate-class0.4020.0080.411
ddpcrWell-class0.030.000.03
ddpcrWell-methods0.3450.0030.348
dropletPlot4.3510.1954.558
exportTable0.2020.0220.226
extractPlateName0.0000.0010.001
extractWellNames0.0000.0000.001
facetPlot2.4340.0552.496
flatPlot3.9760.2004.208
fullCopiesSummary0.0130.0030.016
fullCountsSummary0.0470.0080.056
ggplot.well6.4300.2196.664
gridClassify5.3200.1235.455
heatPlot1.5800.0361.623
kmeansClassify1.4380.0351.473
knnClassify8.1350.1598.309
mahalanobisRain0.8420.0330.878
mutantCopiesSummary0.0060.0010.008
numDroplets0.4600.0080.469
parseClusterCounts0.0230.0060.029
plateClassification1.4950.0281.525
plateClassificationMethod0.5550.0070.563
plateSummary1.8560.0141.873
positiveCounts0.0400.0010.040
readCSVDataFrame0.0190.0040.024
relabelClasses0.0640.0010.066
removeDropletClasses0.6710.0180.691
renormalisePlate4.0200.0684.096
sdRain2.8060.0182.828
setChannelNames0.0020.0010.003
setDropletVolume0.0000.0000.001
sortDataFrame0.0040.0020.005
sortWells0.4210.0020.423
thresholdClassify2.2310.0282.262
wellClassification0.0310.0020.033
wellClassificationMethod0.0410.0010.042
whiteTheme1.5100.0361.549
wildTypeCopiesSummary0.0090.0020.011