Package: twoddpcr

Version: 1.10.0

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_1.10.0.tar.gz

StartedAt: 2020-04-15 06:20:03 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 06:22:45 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 162.4 seconds

RetCode: 0

Status:  OK

CheckDir: twoddpcr.Rcheck

Warnings: 0

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### Running command:
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###   /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_1.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/twoddpcr.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘twoddpcr/DESCRIPTION’ ... OK
* this is package ‘twoddpcr’ version ‘1.10.0’
* 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 or elapsed time > 5s
                   user system elapsed
knnClassify      10.236  0.377  10.843
ggplot.well       7.949  0.427   9.754
dropletPlot       5.877  0.436   7.161
flatPlot          5.867  0.351   6.311
renormalisePlate  5.622  0.294   5.965
* 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

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL twoddpcr
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/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)

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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 
  9.343   0.596   9.983 

name	user	system	elapsed
amplitudes	0.630	0.044	0.682
basicsSummary	0.007	0.000	0.008
castSummary	0.034	0.004	0.038
classCov	0.094	0.015	0.108
classMeans	0.094	0.014	0.109
classStats	0.120	0.020	0.142
clusterCentres	1.354	0.087	1.448
copiesSummary	0.007	0.000	0.008
ddpcrPlate-class	0.456	0.017	0.476
ddpcrWell-class	0.031	0.001	0.032
ddpcrWell-methods	0.426	0.019	0.453
dropletPlot	5.877	0.436	7.161
exportTable	0.257	0.014	0.445
extractPlateName	0.001	0.001	0.001
extractWellNames	0.001	0.000	0.002
facetPlot	3.286	0.206	4.022
flatPlot	5.867	0.351	6.311
fullCopiesSummary	0.013	0.001	0.015
fullCountsSummary	0.054	0.005	0.059
ggplot.well	7.949	0.427	9.754
gridClassify	2.889	0.123	3.088
heatPlot	2.495	0.170	2.688
kmeansClassify	1.439	0.101	1.557
knnClassify	10.236	0.377	10.843
mahalanobisRain	0.893	0.086	0.987
mutantCopiesSummary	0.008	0.000	0.008
numDroplets	0.509	0.014	0.527
parseClusterCounts	0.023	0.002	0.025
plateClassification	1.689	0.061	1.779
plateClassificationMethod	0.596	0.016	0.624
plateSummary	2.120	0.027	2.168
positiveCounts	0.035	0.001	0.036
readCSVDataFrame	0.016	0.001	0.018
relabelClasses	0.121	0.007	0.127
removeDropletClasses	1.003	0.077	1.086
renormalisePlate	5.622	0.294	5.965
sdRain	3.183	0.094	3.291
setChannelNames	0.002	0.001	0.002
setDropletVolume	0.000	0.000	0.001
sortDataFrame	0.002	0.001	0.003
sortWells	0.491	0.013	0.505
thresholdClassify	2.203	0.104	2.321
wellClassification	0.039	0.002	0.042
wellClassificationMethod	0.034	0.001	0.036
whiteTheme	1.693	0.028	1.732
wildTypeCopiesSummary	0.009	0.001	0.009