Package: twoddpcr

Version: 1.8.0

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_1.8.0.tar.gz

StartedAt: 2019-10-16 07:36:32 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 07:39:48 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 195.2 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_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/twoddpcr.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.8.0’
* 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      11.785  0.372  13.815
ggplot.well       8.415  0.656   9.084
flatPlot          6.886  0.633   9.278
renormalisePlate  6.601  0.697   7.297
dropletPlot       6.468  0.449   8.829
heatPlot          3.868  0.249   5.945
* 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 3.6.1 (2019-07-05) -- "Action of the Toes"
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 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 10.554   1.281  11.786 

name	user	system	elapsed
amplitudes	0.795	0.078	0.873
basicsSummary	0.012	0.002	0.015
castSummary	0.053	0.014	0.066
classCov	0.254	0.046	0.299
classMeans	0.112	0.021	0.132
classStats	0.125	0.033	0.158
clusterCentres	1.323	0.190	1.513
copiesSummary	0.015	0.002	0.017
ddpcrPlate-class	0.543	0.035	0.580
ddpcrWell-class	0.058	0.008	0.067
ddpcrWell-methods	0.476	0.043	0.520
dropletPlot	6.468	0.449	8.829
exportTable	0.285	0.026	0.316
extractPlateName	0.000	0.001	0.001
extractWellNames	0.001	0.001	0.002
facetPlot	3.695	0.258	3.955
flatPlot	6.886	0.633	9.278
fullCopiesSummary	0.018	0.003	0.021
fullCountsSummary	0.078	0.012	0.090
ggplot.well	8.415	0.656	9.084
gridClassify	3.220	0.235	3.459
heatPlot	3.868	0.249	5.945
kmeansClassify	1.809	0.258	2.067
knnClassify	11.785	0.372	13.815
mahalanobisRain	1.084	0.164	1.484
mutantCopiesSummary	0.011	0.001	0.012
numDroplets	0.508	0.040	0.547
parseClusterCounts	0.028	0.003	0.031
plateClassification	2.048	0.171	2.219
plateClassificationMethod	0.746	0.039	0.784
plateSummary	2.588	0.082	2.670
positiveCounts	0.046	0.008	0.053
readCSVDataFrame	0.023	0.004	0.027
relabelClasses	0.158	0.023	0.181
removeDropletClasses	1.274	0.201	1.476
renormalisePlate	6.601	0.697	7.297
sdRain	3.560	0.218	3.778
setChannelNames	0.002	0.000	0.002
setDropletVolume	0	0	0
sortDataFrame	0.003	0.001	0.003
sortWells	0.482	0.027	0.508
thresholdClassify	2.640	0.221	2.860
wellClassification	0.059	0.007	0.067
wellClassificationMethod	0.040	0.001	0.042
whiteTheme	1.702	0.054	1.757
wildTypeCopiesSummary	0.006	0.000	0.007