BioC 3.5: CHECK report for twoddpcr on oaxaca

Package: twoddpcr

Version: 0.99.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings twoddpcr_0.99.1.tar.gz

StartedAt: 2017-03-04 10:17:45 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 10:19:43 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 118.0 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_0.99.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/twoddpcr.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘twoddpcr/DESCRIPTION’ ... OK
* this is package ‘twoddpcr’ version ‘0.99.1’
* 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 8.058  0.144   8.232
dropletPlot 6.099  0.154   6.316
ggplot.well 5.644  0.251   5.939
* 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	0.581	0.021	0.602
basicsSummary	0.009	0.000	0.010
castSummary	0.124	0.006	0.129
classCov	0.143	0.003	0.145
classMeans	0.123	0.003	0.127
classStats	0.247	0.002	0.251
clusterCentres	1.447	0.036	1.485
copiesSummary	0.063	0.001	0.063
ddpcrPlate-class	0.457	0.009	0.467
ddpcrWell-class	0.048	0.002	0.050
ddpcrWell-methods	0.368	0.012	0.381
dropletPlot	6.099	0.154	6.316
exportTable	0.127	0.008	0.136
extractPlateName	0.001	0.000	0.001
extractWellNames	0.002	0.000	0.002
facetPlot	3.566	0.095	3.680
flatPlot	4.119	0.236	4.393
fullCopiesSummary	0.024	0.001	0.024
fullCountsSummary	0.056	0.004	0.060
ggplot.well	5.644	0.251	5.939
gridClassify	1.905	0.131	2.065
heatPlot	2.785	0.134	2.933
kmeansClassify	1.671	0.117	1.788
knnClassify	8.058	0.144	8.232
mahalanobisRain	0.987	0.138	1.125
mutantCopiesSummary	0.005	0.000	0.006
numDroplets	0.455	0.026	0.481
parseClusterCounts	0.022	0.002	0.023
plateClassification	1.336	0.093	1.431
plateClassificationMethod	0.491	0.017	0.507
plateSummary	1.856	0.036	1.893
positiveCounts	0.093	0.004	0.097
readCSVDataFrame	0.015	0.002	0.017
relabelClasses	0.124	0.008	0.132
removeDropletClasses	0.946	0.095	1.042
renormalisePlate	3.709	0.311	4.021
sdRain	2.663	0.129	2.792
setChannelNames	0.002	0.001	0.002
setDropletVolume	0.001	0.000	0.001
sortDataFrame	0.004	0.000	0.004
sortWells	0.430	0.022	0.452
thresholdClassify	1.835	0.123	1.958
wellClassification	0.023	0.001	0.024
wellClassificationMethod	0.020	0.001	0.021
whiteTheme	1.405	0.037	1.443
wildTypeCopiesSummary	0.008	0.000	0.009