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CHECK report for twoddpcr on malbec1

This page was generated on 2021-05-06 12:29:35 -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: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:twoddpcr.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings twoddpcr_1.14.0.tar.gz
StartedAt: 2021-05-06 06:55:08 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 06:57:44 -0400 (Thu, 06 May 2021)
EllapsedTime: 156.0 seconds
RetCode: 0
Status:   OK  
CheckDir: twoddpcr.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:twoddpcr.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings twoddpcr_1.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/twoddpcr.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (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  9.948  0.024   9.988
ggplot.well  7.552  0.108   7.665
gridClassify 6.640  0.040   6.687
flatPlot     5.948  0.048   6.013
dropletPlot  5.112  0.052   5.171
* 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:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL twoddpcr
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/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-pc-linux-gnu (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 
 10.932   0.196  11.154 

Example timings

twoddpcr.Rcheck/twoddpcr-Ex.timings

nameusersystemelapsed
amplitudes0.7520.0280.783
basicsSummary0.0080.0000.006
castSummary0.0240.0000.022
classCov0.0560.0000.056
classMeans0.0720.0040.074
classStats0.0960.0040.100
clusterCentres1.1440.0041.151
copiesSummary0.0080.0000.005
ddpcrPlate-class0.4480.0000.458
ddpcrWell-class0.0320.0000.034
ddpcrWell-methods0.5080.0040.511
dropletPlot5.1120.0525.171
exportTable0.1360.0080.162
extractPlateName0.0000.0000.001
extractWellNames0.0000.0000.001
facetPlot3.3000.0683.370
flatPlot5.9480.0486.013
fullCopiesSummary0.0040.0000.006
fullCountsSummary0.0320.0000.031
ggplot.well7.5520.1087.665
gridClassify6.6400.0406.687
heatPlot2.2320.0162.253
kmeansClassify1.9160.0001.922
knnClassify9.9480.0249.988
mahalanobisRain1.2080.0001.207
mutantCopiesSummary0.0080.0000.008
numDroplets0.4800.0000.483
parseClusterCounts0.0080.0040.013
plateClassification1.3880.0001.389
plateClassificationMethod0.4920.0000.493
plateSummary3.0720.0003.077
positiveCounts0.0400.0040.042
readCSVDataFrame0.020.000.02
relabelClasses0.3520.0000.351
removeDropletClasses1.0400.0001.047
renormalisePlate4.6840.0004.688
sdRain4.2960.0044.309
setChannelNames0.0000.0000.001
setDropletVolume000
sortDataFrame0.0040.0000.002
sortWells0.6600.0000.662
thresholdClassify3.3280.0003.336
wellClassification0.0480.0000.051
wellClassificationMethod0.0520.0000.051
whiteTheme1.6600.0041.667
wildTypeCopiesSummary0.0040.0000.004