Package: twoddpcr

Version: 1.6.0

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_1.6.0.tar.gz

StartedAt: 2019-04-16 03:17:28 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 03:19:57 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 148.7 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_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/twoddpcr.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.6.0’
* 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      10.912  0.339  11.462
ggplot.well       6.040  0.272   6.373
renormalisePlate  4.965  0.322   5.311
flatPlot          4.679  0.313   5.053
* 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/3.5/Resources/library’
* installing *source* package ‘twoddpcr’ ...
** 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
* DONE (twoddpcr)

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 10.583   0.762  11.389 

name	user	system	elapsed
amplitudes	0.635	0.043	0.680
basicsSummary	0.010	0.002	0.011
castSummary	0.029	0.004	0.032
classCov	0.082	0.008	0.090
classMeans	0.076	0.013	0.089
classStats	0.103	0.014	0.119
clusterCentres	1.080	0.089	1.176
copiesSummary	0.007	0.000	0.007
ddpcrPlate-class	0.456	0.018	0.477
ddpcrWell-class	0.049	0.002	0.051
ddpcrWell-methods	0.481	0.009	0.494
dropletPlot	4.614	0.199	4.862
exportTable	0.193	0.011	0.206
extractPlateName	0.000	0.000	0.001
extractWellNames	0.001	0.000	0.001
facetPlot	3.296	0.127	3.471
flatPlot	4.679	0.313	5.053
fullCopiesSummary	0.013	0.001	0.014
fullCountsSummary	0.070	0.006	0.078
ggplot.well	6.040	0.272	6.373
gridClassify	2.776	0.170	2.984
heatPlot	2.327	0.119	2.481
kmeansClassify	1.571	0.116	1.699
knnClassify	10.912	0.339	11.462
mahalanobisRain	1.066	0.089	1.166
mutantCopiesSummary	0.01	0.00	0.01
numDroplets	0.559	0.015	0.577
parseClusterCounts	0.022	0.002	0.024
plateClassification	1.930	0.103	2.040
plateClassificationMethod	0.602	0.022	0.629
plateSummary	2.311	0.040	2.363
positiveCounts	0.036	0.002	0.038
readCSVDataFrame	0.020	0.002	0.022
relabelClasses	0.135	0.004	0.142
removeDropletClasses	1.119	0.076	1.202
renormalisePlate	4.965	0.322	5.311
sdRain	3.150	0.133	3.303
setChannelNames	0.002	0.000	0.002
setDropletVolume	0.000	0.001	0.000
sortDataFrame	0.002	0.000	0.003
sortWells	0.531	0.009	0.543
thresholdClassify	2.833	0.135	2.981
wellClassification	0.043	0.000	0.044
wellClassificationMethod	0.045	0.001	0.047
whiteTheme	1.687	0.036	1.730
wildTypeCopiesSummary	0.009	0.000	0.009