Package: twoddpcr

Version: 1.4.1

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_1.4.1.tar.gz

StartedAt: 2018-10-17 00:33:34 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 00:36:07 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 153.2 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_1.4.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/twoddpcr.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.4.1’
* 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      10.142  0.175  10.414
ggplot.well       6.014  0.255   6.344
renormalisePlate  5.016  0.315   5.345
flatPlot          4.959  0.299   5.323
* 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 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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 
 10.681   0.807  11.544 

name	user	system	elapsed
amplitudes	0.941	0.058	1.672
basicsSummary	0.013	0.001	0.024
castSummary	0.047	0.009	0.098
classCov	0.107	0.011	0.200
classMeans	0.109	0.010	0.198
classStats	0.127	0.012	0.235
clusterCentres	1.270	0.103	1.636
copiesSummary	0.013	0.001	0.014
ddpcrPlate-class	0.495	0.020	0.530
ddpcrWell-class	0.038	0.004	0.044
ddpcrWell-methods	0.516	0.009	0.529
dropletPlot	4.703	0.221	4.985
exportTable	0.181	0.009	0.193
extractPlateName	0.003	0.000	0.002
extractWellNames	0.002	0.000	0.003
facetPlot	3.647	0.172	4.946
flatPlot	4.959	0.299	5.323
fullCopiesSummary	0.027	0.001	0.027
fullCountsSummary	0.043	0.003	0.046
ggplot.well	6.014	0.255	6.344
gridClassify	2.819	0.148	3.008
heatPlot	2.143	0.120	2.282
kmeansClassify	1.529	0.109	1.644
knnClassify	10.142	0.175	10.414
mahalanobisRain	0.903	0.092	1.002
mutantCopiesSummary	0.006	0.001	0.007
numDroplets	0.582	0.022	0.606
parseClusterCounts	0.025	0.002	0.027
plateClassification	1.639	0.114	1.759
plateClassificationMethod	0.595	0.020	0.621
plateSummary	2.096	0.031	2.140
positiveCounts	0.075	0.003	0.078
readCSVDataFrame	0.022	0.002	0.024
relabelClasses	0.057	0.003	0.059
removeDropletClasses	0.770	0.071	0.843
renormalisePlate	5.016	0.315	5.345
sdRain	3.378	0.145	3.553
setChannelNames	0.005	0.001	0.006
setDropletVolume	0.001	0.000	0.003
sortDataFrame	0.005	0.000	0.005
sortWells	0.549	0.020	0.572
thresholdClassify	2.633	0.138	2.785
wellClassification	0.046	0.001	0.047
wellClassificationMethod	0.044	0.001	0.045
whiteTheme	1.910	0.044	1.977
wildTypeCopiesSummary	0.009	0.000	0.010