Package: twoddpcr

Version: 1.7.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:twoddpcr.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings twoddpcr_1.7.0.tar.gz

StartedAt: 2019-04-09 04:12:57 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 04:15:16 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 138.7 seconds

RetCode: 0

Status:  OK

CheckDir: twoddpcr.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:twoddpcr.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings twoddpcr_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/twoddpcr.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (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      8.793  0.135   8.929
dropletPlot      6.017  0.084   6.101
ggplot.well      5.952  0.048   6.000
flatPlot         5.922  0.073   5.994
renormalisePlate 5.565  0.000   5.567
* 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:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL twoddpcr
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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-pc-linux-gnu (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 
 10.286   0.171  10.446 

name	user	system	elapsed
amplitudes	0.961	0.012	0.973
basicsSummary	0.01	0.00	0.01
castSummary	0.024	0.004	0.029
classCov	0.083	0.000	0.083
classMeans	0.105	0.000	0.105
classStats	0.099	0.004	0.103
clusterCentres	1.665	0.016	1.681
copiesSummary	0.007	0.000	0.007
ddpcrPlate-class	0.607	0.004	0.611
ddpcrWell-class	0.050	0.003	0.053
ddpcrWell-methods	0.597	0.000	0.597
dropletPlot	6.017	0.084	6.101
exportTable	0.190	0.016	0.211
extractPlateName	0.001	0.000	0.001
extractWellNames	0.001	0.000	0.000
facetPlot	2.549	0.035	2.585
flatPlot	5.922	0.073	5.994
fullCopiesSummary	0.007	0.000	0.006
fullCountsSummary	0.025	0.004	0.028
ggplot.well	5.952	0.048	6.000
gridClassify	3.035	0.008	3.042
heatPlot	2.124	0.016	2.139
kmeansClassify	1.781	0.000	1.781
knnClassify	8.793	0.135	8.929
mahalanobisRain	0.943	0.001	0.943
mutantCopiesSummary	0.004	0.000	0.005
numDroplets	0.421	0.000	0.421
parseClusterCounts	0.015	0.000	0.015
plateClassification	1.595	0.000	1.595
plateClassificationMethod	0.738	0.000	0.746
plateSummary	3.678	0.000	3.683
positiveCounts	0.086	0.000	0.086
readCSVDataFrame	0.013	0.003	0.017
relabelClasses	0.073	0.000	0.072
removeDropletClasses	1.187	0.000	1.188
renormalisePlate	5.565	0.000	5.567
sdRain	4.333	0.003	4.351
setChannelNames	0.002	0.000	0.002
setDropletVolume	0	0	0
sortDataFrame	0.003	0.000	0.003
sortWells	0.632	0.000	0.632
thresholdClassify	2.634	0.003	2.638
wellClassification	0.044	0.000	0.044
wellClassificationMethod	0.035	0.000	0.035
whiteTheme	1.310	0.008	1.318
wildTypeCopiesSummary	0.004	0.000	0.004