BioC 3.6: CHECK report for twoddpcr on malbec1

Package: twoddpcr

Version: 1.1.3

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings twoddpcr_1.1.3.tar.gz

StartedAt: 2017-08-16 02:56:06 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 02:57:59 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 112.7 seconds

RetCode: 0

Status:  OK

CheckDir: twoddpcr.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings twoddpcr_1.1.3.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/twoddpcr.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.1.3’
* 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 7.284  0.012   7.296
dropletPlot 5.384  0.016   5.404
flatPlot    5.112  0.068   5.185
* 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	0.564	0.008	0.569
basicsSummary	0.004	0.000	0.006
castSummary	0.064	0.000	0.064
classCov	0.24	0.00	0.24
classMeans	0.096	0.000	0.096
classStats	0.116	0.000	0.117
clusterCentres	1.172	0.004	1.178
copiesSummary	0.04	0.00	0.04
ddpcrPlate-class	0.436	0.004	0.441
ddpcrWell-class	0.044	0.000	0.045
ddpcrWell-methods	0.472	0.004	0.479
dropletPlot	5.384	0.016	5.404
exportTable	0.100	0.000	0.104
extractPlateName	0	0	0
extractWellNames	0.004	0.000	0.001
facetPlot	3.048	0.032	3.084
flatPlot	5.112	0.068	5.185
fullCopiesSummary	0.016	0.000	0.016
fullCountsSummary	0.028	0.000	0.029
ggplot.well	4.716	0.048	4.767
gridClassify	1.932	0.016	1.946
heatPlot	2.128	0.000	2.130
kmeansClassify	1.360	0.000	1.359
knnClassify	7.284	0.012	7.296
mahalanobisRain	0.808	0.000	0.811
mutantCopiesSummary	0.008	0.000	0.005
numDroplets	0.34	0.00	0.34
parseClusterCounts	0.012	0.000	0.011
plateClassification	1.096	0.004	1.101
plateClassificationMethod	0.300	0.000	0.297
plateSummary	2.248	0.000	2.248
positiveCounts	0.044	0.000	0.043
readCSVDataFrame	0.012	0.000	0.013
relabelClasses	0.100	0.000	0.098
removeDropletClasses	0.784	0.000	0.787
renormalisePlate	3.904	0.000	3.906
sdRain	3.252	0.000	3.254
setChannelNames	0.000	0.000	0.002
setDropletVolume	0.000	0.000	0.001
sortDataFrame	0.000	0.000	0.002
sortWells	0.344	0.000	0.347
thresholdClassify	1.624	0.000	1.623
wellClassification	0.028	0.000	0.028
wellClassificationMethod	0.032	0.000	0.030
whiteTheme	1.236	0.016	1.252
wildTypeCopiesSummary	0.004	0.000	0.005