Package: twoddpcr

Version: 1.7.0

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_1.7.0.tar.gz

StartedAt: 2019-04-09 06:10:27 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 06:13:28 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 181.0 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_1.7.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/twoddpcr.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.7.0’
* 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      10.956  0.323  11.288
ggplot.well       6.084  0.541   7.768
renormalisePlate  5.530  0.607   6.137
flatPlot          4.844  0.497   5.369
dropletPlot       4.726  0.367   5.103
facetPlot         3.954  0.320   5.926
* 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 Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
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 
 10.955   1.310  12.212 

name	user	system	elapsed
amplitudes	0.782	0.082	0.864
basicsSummary	0.012	0.001	0.013
castSummary	0.028	0.008	0.036
classCov	0.064	0.008	0.072
classMeans	0.110	0.038	0.147
classStats	0.135	0.022	0.157
clusterCentres	1.331	0.178	1.509
copiesSummary	0.014	0.001	0.015
ddpcrPlate-class	0.482	0.046	0.529
ddpcrWell-class	0.041	0.004	0.047
ddpcrWell-methods	0.404	0.044	0.449
dropletPlot	4.726	0.367	5.103
exportTable	0.238	0.023	0.358
extractPlateName	0.001	0.000	0.001
extractWellNames	0.001	0.000	0.001
facetPlot	3.954	0.320	5.926
flatPlot	4.844	0.497	5.369
fullCopiesSummary	0.017	0.003	0.019
fullCountsSummary	0.068	0.011	0.078
ggplot.well	6.084	0.541	7.768
gridClassify	3.492	0.242	4.445
heatPlot	2.792	0.249	3.045
kmeansClassify	1.973	0.256	2.229
knnClassify	10.956	0.323	11.288
mahalanobisRain	1.091	0.203	1.295
mutantCopiesSummary	0.009	0.001	0.010
numDroplets	0.469	0.040	0.510
parseClusterCounts	0.030	0.004	0.034
plateClassification	1.724	0.123	1.846
plateClassificationMethod	0.753	0.062	0.815
plateSummary	1.988	0.064	2.078
positiveCounts	0.042	0.002	0.043
readCSVDataFrame	0.023	0.009	0.034
relabelClasses	0.079	0.013	0.093
removeDropletClasses	0.955	0.168	1.123
renormalisePlate	5.530	0.607	6.137
sdRain	2.693	0.168	2.861
setChannelNames	0.002	0.001	0.002
setDropletVolume	0.000	0.000	0.001
sortDataFrame	0.002	0.000	0.003
sortWells	0.482	0.041	0.523
thresholdClassify	2.470	0.217	2.687
wellClassification	0.037	0.005	0.042
wellClassificationMethod	0.030	0.002	0.033
whiteTheme	1.656	0.062	1.717
wildTypeCopiesSummary	0.005	0.001	0.006