BioC 3.5: CHECK report for twoddpcr on veracruz2

Package: twoddpcr

Version: 1.0.6

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings twoddpcr_1.0.6.tar.gz

StartedAt: 2017-08-16 09:06:30 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 09:08:30 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 120.4 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_1.0.6.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-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 ‘1.0.6’
* 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 9.737  0.163  10.186
ggplot.well 5.591  0.272   6.378
dropletPlot 5.671  0.154   6.007
* 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	0.603	0.021	0.653
basicsSummary	0.007	0.000	0.008
castSummary	0.101	0.005	0.107
classCov	0.176	0.004	0.180
classMeans	0.170	0.004	0.177
classStats	0.127	0.003	0.130
clusterCentres	1.241	0.027	1.315
copiesSummary	0.048	0.001	0.052
ddpcrPlate-class	0.376	0.008	0.394
ddpcrWell-class	0.066	0.001	0.070
ddpcrWell-methods	0.444	0.009	0.470
dropletPlot	5.671	0.154	6.007
exportTable	0.142	0.006	0.151
extractPlateName	0.001	0.000	0.000
extractWellNames	0.001	0.000	0.002
facetPlot	3.297	0.092	3.481
flatPlot	4.066	0.234	4.411
fullCopiesSummary	0.028	0.001	0.028
fullCountsSummary	0.056	0.003	0.059
ggplot.well	5.591	0.272	6.378
gridClassify	2.105	0.156	2.412
heatPlot	2.807	0.105	3.095
kmeansClassify	1.406	0.081	1.526
knnClassify	9.737	0.163	10.186
mahalanobisRain	0.859	0.115	0.992
mutantCopiesSummary	0.004	0.000	0.004
numDroplets	0.369	0.018	0.402
parseClusterCounts	0.015	0.001	0.016
plateClassification	1.234	0.080	1.350
plateClassificationMethod	0.366	0.025	0.401
plateSummary	1.865	0.029	1.940
positiveCounts	0.052	0.003	0.056
readCSVDataFrame	0.018	0.001	0.020
relabelClasses	0.141	0.006	0.148
removeDropletClasses	0.746	0.074	0.825
renormalisePlate	3.717	0.265	4.045
sdRain	2.473	0.123	2.626
setChannelNames	0.002	0.001	0.002
setDropletVolume	0.001	0.000	0.000
sortDataFrame	0.003	0.000	0.003
sortWells	0.346	0.022	0.373
thresholdClassify	1.698	0.111	1.827
wellClassification	0.018	0.000	0.018
wellClassificationMethod	0.019	0.001	0.020
whiteTheme	1.158	0.030	1.202
wildTypeCopiesSummary	0.005	0.000	0.005