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CHECK report for twoddpcr on machv2

This page was generated on 2020-10-17 11:59:50 -0400 (Sat, 17 Oct 2020).

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 1850/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
twoddpcr 1.12.0
Anthony Chiu
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/twoddpcr
Branch: RELEASE_3_11
Last Commit: b8f2809
Last Changed Date: 2020-04-27 15:05:36 -0400 (Mon, 27 Apr 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  NA 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: twoddpcr
Version: 1.12.0
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_1.12.0.tar.gz
StartedAt: 2020-10-17 06:08:03 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 06:11:08 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 184.5 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_1.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/twoddpcr.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.12.0’
* 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      10.166  0.150  10.329
ggplot.well       7.959  0.237   8.210
gridClassify      6.462  0.127   6.601
renormalisePlate  5.376  0.111   5.491
dropletPlot       4.909  0.233   5.158
* 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 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 156 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 11.562   0.579  12.134 

Example timings

twoddpcr.Rcheck/twoddpcr-Ex.timings

nameusersystemelapsed
amplitudes0.6520.0400.692
basicsSummary0.0120.0020.014
castSummary0.0330.0100.042
classCov0.0860.0120.097
classMeans0.1060.0110.117
classStats0.0930.0210.114
clusterCentres1.1410.0631.205
copiesSummary0.0070.0010.009
ddpcrPlate-class0.4080.0070.416
ddpcrWell-class0.0460.0020.048
ddpcrWell-methods0.4580.0080.466
dropletPlot4.9090.2335.158
exportTable0.2320.0220.257
extractPlateName000
extractWellNames0.0010.0010.001
facetPlot3.0400.0673.110
flatPlot4.6760.2184.899
fullCopiesSummary0.0130.0030.016
fullCountsSummary0.0470.0090.056
ggplot.well7.9590.2378.210
gridClassify6.4620.1276.601
heatPlot1.9350.0561.995
kmeansClassify1.7070.0491.757
knnClassify10.166 0.15010.329
mahalanobisRain0.9930.0231.018
mutantCopiesSummary0.0090.0020.010
numDroplets0.4950.0060.501
parseClusterCounts0.0170.0040.021
plateClassification1.8240.0341.858
plateClassificationMethod0.6750.0060.682
plateSummary2.3380.0172.359
positiveCounts0.1110.0030.114
readCSVDataFrame0.0170.0030.020
relabelClasses0.0790.0020.081
removeDropletClasses1.1640.0251.190
renormalisePlate5.3760.1115.491
sdRain3.5390.0373.578
setChannelNames0.0020.0010.004
setDropletVolume0.0010.0000.001
sortDataFrame0.0030.0020.005
sortWells0.4710.0050.476
thresholdClassify2.2720.0272.301
wellClassification0.0350.0010.037
wellClassificationMethod0.0290.0000.030
whiteTheme1.7270.0401.777
wildTypeCopiesSummary0.0080.0020.010