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: 2017-10-18 09:58:44 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 10:00:58 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 134.0 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_1.0.6.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/twoddpcr.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 11.102  0.229  12.980
ggplot.well  5.896  0.321   7.786
dropletPlot  5.592  0.193   6.070
flatPlot     4.484  0.272   5.543
* 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	0.536	0.019	0.566
basicsSummary	0.009	0.001	0.009
castSummary	0.101	0.007	0.112
classCov	0.191	0.005	0.207
classMeans	0.198	0.004	0.209
classStats	0.143	0.004	0.150
clusterCentres	1.389	0.030	1.495
copiesSummary	0.046	0.001	0.050
ddpcrPlate-class	0.343	0.009	0.365
ddpcrWell-class	0.062	0.001	0.069
ddpcrWell-methods	0.401	0.003	0.418
dropletPlot	5.592	0.193	6.070
exportTable	0.113	0.005	0.125
extractPlateName	0.000	0.000	0.001
extractWellNames	0.001	0.001	0.001
facetPlot	3.496	0.093	3.774
flatPlot	4.484	0.272	5.543
fullCopiesSummary	0.026	0.001	0.030
fullCountsSummary	0.049	0.004	0.077
ggplot.well	5.896	0.321	7.786
gridClassify	2.382	0.156	3.143
heatPlot	3.104	0.133	4.207
kmeansClassify	1.757	0.102	2.441
knnClassify	11.102	0.229	12.980
mahalanobisRain	0.873	0.103	1.046
mutantCopiesSummary	0.007	0.000	0.007
numDroplets	0.421	0.010	0.457
parseClusterCounts	0.017	0.001	0.020
plateClassification	1.257	0.061	1.363
plateClassificationMethod	0.374	0.017	0.403
plateSummary	1.967	0.019	2.082
positiveCounts	0.087	0.002	0.092
readCSVDataFrame	0.018	0.002	0.024
relabelClasses	0.141	0.004	0.152
removeDropletClasses	0.968	0.065	1.072
renormalisePlate	4.353	0.250	4.792
sdRain	3.172	0.139	3.406
setChannelNames	0.002	0.000	0.003
setDropletVolume	0.001	0.000	0.001
sortDataFrame	0.003	0.000	0.004
sortWells	0.413	0.019	0.454
thresholdClassify	2.180	0.096	2.340
wellClassification	0.030	0.001	0.032
wellClassificationMethod	0.042	0.002	0.044
whiteTheme	1.419	0.034	1.507
wildTypeCopiesSummary	0.016	0.001	0.017