Multiple platform build/check report for BioC 3.11 - CHECK report for twoddpcr on celaya2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:twoddpcr.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings twoddpcr_1.11.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/twoddpcr.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.11.0’
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
knnClassify      11.193  0.358  13.481
ggplot.well       7.739  0.503  10.076
flatPlot          6.756  0.568   7.340
dropletPlot       6.139  0.524   6.698
renormalisePlate  5.685  0.670   7.711
facetPlot         3.881  0.242   5.957
* 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

Installation output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL twoddpcr
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘twoddpcr’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (twoddpcr)

Tests output


R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(twoddpcr)
> 
> test_check("twoddpcr")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 156 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 11.169   1.142  12.259

Example timings

name	user	system	elapsed
amplitudes	0.644	0.084	0.727
basicsSummary	0.015	0.004	0.020
castSummary	0.062	0.019	0.080
classCov	0.123	0.045	0.168
classMeans	0.099	0.017	0.116
classStats	0.114	0.031	0.144
clusterCentres	1.286	0.149	1.435
copiesSummary	0.008	0.001	0.009
ddpcrPlate-class	0.405	0.027	0.435
ddpcrWell-class	0.069	0.007	0.078
ddpcrWell-methods	0.542	0.043	0.585
dropletPlot	6.139	0.524	6.698
exportTable	0.285	0.030	0.465
extractPlateName	0.001	0.001	0.002
extractWellNames	0.002	0.000	0.002
facetPlot	3.881	0.242	5.957
flatPlot	6.756	0.568	7.340
fullCopiesSummary	0.010	0.002	0.011
fullCountsSummary	0.044	0.007	0.052
ggplot.well	7.739	0.503	10.076
gridClassify	3.201	0.210	3.428
heatPlot	3.644	0.247	3.898
kmeansClassify	1.797	0.255	2.053
knnClassify	11.193	0.358	13.481
mahalanobisRain	0.897	0.151	1.048
mutantCopiesSummary	0.006	0.001	0.007
numDroplets	0.470	0.031	0.501
parseClusterCounts	0.027	0.003	0.029
plateClassification	1.961	0.176	2.136
plateClassificationMethod	0.664	0.033	0.696
plateSummary	2.473	0.094	2.568
positiveCounts	0.028	0.002	0.030
readCSVDataFrame	0.017	0.002	0.020
relabelClasses	0.055	0.009	0.064
removeDropletClasses	1.044	0.177	1.724
renormalisePlate	5.685	0.670	7.711
sdRain	3.715	0.208	3.924
setChannelNames	0.002	0.000	0.002
setDropletVolume	0.000	0.001	0.000
sortDataFrame	0.004	0.001	0.005
sortWells	0.634	0.047	0.682
thresholdClassify	2.621	0.213	2.834
wellClassification	0.051	0.003	0.055
wellClassificationMethod	0.039	0.003	0.043
whiteTheme	1.865	0.054	1.919
wildTypeCopiesSummary	0.006	0.001	0.007

CHECK report for twoddpcr on celaya2

Summary

Command output

Installation output

Tests output

Example timings