BioC 3.6: CHECK report for twoddpcr on veracruz1

Package: twoddpcr

Version: 1.1.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings twoddpcr_1.1.3.tar.gz

StartedAt: 2017-08-16 09:22:23 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 09:24:26 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 123.5 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 --no-vignettes --timings twoddpcr_1.1.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/twoddpcr.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.1.3’
* 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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
knnClassify 9.044  0.143   9.390
dropletPlot 5.271  0.154   5.570
ggplot.well 5.068  0.241   5.506
* 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

* installing *source* package ‘twoddpcr’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (twoddpcr)

name	user	system	elapsed
amplitudes	0.594	0.018	0.636
basicsSummary	0.008	0.000	0.009
castSummary	0.064	0.004	0.067
classCov	0.144	0.004	0.147
classMeans	0.168	0.002	0.173
classStats	0.150	0.005	0.158
clusterCentres	1.232	0.026	1.285
copiesSummary	0.059	0.000	0.060
ddpcrPlate-class	0.326	0.006	0.339
ddpcrWell-class	0.061	0.000	0.064
ddpcrWell-methods	0.403	0.013	0.421
dropletPlot	5.271	0.154	5.570
exportTable	0.127	0.006	0.140
extractPlateName	0.000	0.000	0.001
extractWellNames	0.001	0.000	0.001
facetPlot	3.111	0.085	3.292
flatPlot	4.104	0.229	4.441
fullCopiesSummary	0.020	0.001	0.020
fullCountsSummary	0.043	0.003	0.048
ggplot.well	5.068	0.241	5.506
gridClassify	1.908	0.131	2.115
heatPlot	2.828	0.114	3.055
kmeansClassify	1.393	0.097	1.532
knnClassify	9.044	0.143	9.390
mahalanobisRain	0.780	0.088	0.879
mutantCopiesSummary	0.006	0.000	0.007
numDroplets	0.329	0.018	0.348
parseClusterCounts	0.017	0.001	0.018
plateClassification	1.002	0.079	1.124
plateClassificationMethod	0.323	0.019	0.344
plateSummary	1.821	0.031	1.924
positiveCounts	0.046	0.003	0.051
readCSVDataFrame	0.016	0.001	0.018
relabelClasses	0.127	0.011	0.139
removeDropletClasses	0.738	0.075	0.821
renormalisePlate	3.730	0.233	4.084
sdRain	2.707	0.113	2.908
setChannelNames	0.003	0.000	0.003
setDropletVolume	0.001	0.000	0.001
sortDataFrame	0.003	0.001	0.003
sortWells	0.356	0.017	0.389
thresholdClassify	1.840	0.123	2.010
wellClassification	0.024	0.001	0.027
wellClassificationMethod	0.027	0.001	0.029
whiteTheme	1.358	0.035	1.413
wildTypeCopiesSummary	0.007	0.000	0.008