BioC 3.5: CHECK report for twoddpcr on toluca2

Package: twoddpcr

Version: 0.99.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings twoddpcr_0.99.2.tar.gz

StartedAt: 2017-04-23 11:00:19 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 11:02:50 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 150.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: twoddpcr.Rcheck

Warnings: 1

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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_0.99.2.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 r72187)
* 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 ‘0.99.2’
* 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 ... WARNING
Bad \usage lines found in documentation object 'dropletPlot':
  "\\S4method{dropletPlot}{data.frame}"(droplets, ch1Label = "Ch1 Amplitude",
    ch2Label = "Ch2 Amplitude", cMethod = "None", mapping = aes_string(x =
    "Ch2.Amplitude", y = "Ch1.Amplitude", colour = cMethod),
    finalCentres = NULL, initialCentres = NULL, selectedCentre = NULL,
  <<<<<<< HEAD
    plotLimits = list(x = c(1000, 9000), y = c(3000, 13500)))
  =======
    plotLimits = list(x = c(1000, 9000), y = c(3000, 13500)),
    legendLabels = ddpcr$classesRain)
  >>>>>>> master
  "\\S4method{dropletPlot}{ddpcrWell}"(droplets, ch1Label = "Ch1 Amplitude",
    ch2Label = "Ch2 Amplitude", cMethod = "None", mapping = aes_string(x =
    "Ch2.Amplitude", y = "Ch1.Amplitude", colour = cMethod),
    finalCentres = NULL, initialCentres = NULL, selectedCentre = NULL,
  <<<<<<< HEAD
    plotLimits = list(x = c(1000, 9000), y = c(3000, 13500)))
  =======
    plotLimits = list(x = c(1000, 9000), y = c(3000, 13500)),
    legendLabels = ddpcr$classesRain)
  >>>>>>> master
  "\\S4method{dropletPlot}{ddpcrPlate}"(droplets, ch1Label = "Ch1 Amplitude",
    ch2Label = "Ch2 Amplitude", cMethod = "None", mapping = aes_string(x =
    "Ch2.Amplitude", y = "Ch1.Amplitude", colour = cMethod),
    finalCentres = NULL, initialCentres = NULL, selectedCentre = NULL,
  <<<<<<< HEAD
    plotLimits = list(x = c(1000, 9000), y = c(3000, 13500)))
  =======
    plotLimits = list(x = c(1000, 9000), y = c(3000, 13500)),
    legendLabels = ddpcr$classesRain)
  >>>>>>> master

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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      9.577  0.233   9.851
dropletPlot      6.693  0.289   7.063
ggplot.well      6.013  0.391   6.464
renormalisePlate 5.320  0.288   5.679
flatPlot         4.928  0.278   5.253
* 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: 1 WARNING
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/twoddpcr.Rcheck/00check.log’
for details.

* 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	0.720	0.024	0.746
basicsSummary	0.009	0.001	0.010
castSummary	0.112	0.005	0.118
classCov	0.212	0.003	0.217
classMeans	0.128	0.001	0.129
classStats	0.159	0.001	0.161
clusterCentres	1.549	0.031	1.584
copiesSummary	0.062	0.001	0.063
ddpcrPlate-class	0.542	0.025	0.568
ddpcrWell-class	0.077	0.003	0.080
ddpcrWell-methods	0.414	0.012	0.428
dropletPlot	6.693	0.289	7.063
exportTable	0.167	0.006	0.178
extractPlateName	0.001	0.000	0.001
extractWellNames	0.002	0.000	0.002
facetPlot	3.993	0.087	4.131
flatPlot	4.928	0.278	5.253
fullCopiesSummary	0.028	0.000	0.031
fullCountsSummary	0.051	0.003	0.055
ggplot.well	6.013	0.391	6.464
gridClassify	2.581	0.146	2.748
heatPlot	3.306	0.092	3.475
kmeansClassify	1.655	0.078	1.735
knnClassify	9.577	0.233	9.851
mahalanobisRain	1.074	0.132	1.210
mutantCopiesSummary	0.007	0.000	0.008
numDroplets	0.501	0.033	0.535
parseClusterCounts	0.020	0.002	0.021
plateClassification	1.608	0.088	1.703
plateClassificationMethod	0.458	0.020	0.500
plateSummary	2.216	0.036	2.279
positiveCounts	0.057	0.002	0.059
readCSVDataFrame	0.022	0.002	0.024
relabelClasses	0.138	0.010	0.146
removeDropletClasses	1.258	0.107	1.370
renormalisePlate	5.320	0.288	5.679
sdRain	3.407	0.151	3.571
setChannelNames	0.003	0.001	0.003
setDropletVolume	0.001	0.000	0.001
sortDataFrame	0.003	0.000	0.004
sortWells	0.496	0.025	0.523
thresholdClassify	2.461	0.112	2.597
wellClassification	0.033	0.001	0.034
wellClassificationMethod	0.047	0.003	0.053
whiteTheme	1.465	0.032	1.506
wildTypeCopiesSummary	0.019	0.003	0.021