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 04:17:01 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 04:19:34 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 153.8 seconds

RetCode: 0

Status:  OK

CheckDir: twoddpcr.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running 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
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/twoddpcr.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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      12.017  0.261  12.612
ggplot.well       5.809  0.313   6.328
renormalisePlate  5.550  0.385   6.029
dropletPlot       5.145  0.287   6.796
flatPlot          4.598  0.392   5.212
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL twoddpcr
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/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 Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
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 
 10.349   0.731  11.152 

name	user	system	elapsed
amplitudes	0.660	0.049	0.712
basicsSummary	0.011	0.001	0.011
castSummary	0.031	0.005	0.036
classCov	0.078	0.010	0.089
classMeans	0.082	0.008	0.091
classStats	0.102	0.013	0.115
clusterCentres	1.215	0.092	1.311
copiesSummary	0.007	0.000	0.007
ddpcrPlate-class	0.444	0.018	0.468
ddpcrWell-class	0.037	0.003	0.039
ddpcrWell-methods	0.447	0.015	0.467
dropletPlot	5.145	0.287	6.796
exportTable	0.211	0.025	0.359
extractPlateName	0.000	0.000	0.001
extractWellNames	0.001	0.000	0.001
facetPlot	2.843	0.131	3.050
flatPlot	4.598	0.392	5.212
fullCopiesSummary	0.015	0.001	0.017
fullCountsSummary	0.057	0.005	0.063
ggplot.well	5.809	0.313	6.328
gridClassify	2.669	0.245	3.049
heatPlot	2.184	0.115	2.364
kmeansClassify	1.467	0.118	1.604
knnClassify	12.017	0.261	12.612
mahalanobisRain	0.978	0.081	1.067
mutantCopiesSummary	0.005	0.000	0.005
numDroplets	0.520	0.022	0.546
parseClusterCounts	0.019	0.002	0.021
plateClassification	1.696	0.099	1.817
plateClassificationMethod	0.615	0.022	0.646
plateSummary	2.322	0.054	2.405
positiveCounts	0.087	0.004	0.093
readCSVDataFrame	0.023	0.003	0.026
relabelClasses	0.076	0.004	0.081
removeDropletClasses	1.067	0.088	1.174
renormalisePlate	5.550	0.385	6.029
sdRain	3.238	0.131	3.397
setChannelNames	0.002	0.000	0.001
setDropletVolume	0.001	0.000	0.000
sortDataFrame	0.002	0.000	0.002
sortWells	0.465	0.012	0.487
thresholdClassify	2.300	0.132	2.451
wellClassification	0.028	0.001	0.029
wellClassificationMethod	0.031	0.001	0.032
whiteTheme	1.649	0.037	1.695
wildTypeCopiesSummary	0.006	0.000	0.006