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CHECK report for twoddpcr on merida1

This page was generated on 2020-04-15 12:45:00 -0400 (Wed, 15 Apr 2020).

Package 1770/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
twoddpcr 1.10.0
Anthony Chiu
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/twoddpcr
Branch: RELEASE_3_10
Last Commit: bb6a5aa
Last Changed Date: 2019-10-29 13:10:17 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: twoddpcr
Version: 1.10.0
Command: /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_1.10.0.tar.gz
StartedAt: 2020-04-15 06:20:03 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 06:22:45 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 162.4 seconds
RetCode: 0
Status:  OK 
CheckDir: twoddpcr.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /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_1.10.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/twoddpcr.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.10.0’
* 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 or elapsed time > 5s
                   user system elapsed
knnClassify      10.236  0.377  10.843
ggplot.well       7.949  0.427   9.754
dropletPlot       5.877  0.436   7.161
flatPlot          5.867  0.351   6.311
renormalisePlate  5.622  0.294   5.965
* 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

twoddpcr.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL twoddpcr
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/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

twoddpcr.Rcheck/tests/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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 
  9.343   0.596   9.983 

Example timings

twoddpcr.Rcheck/twoddpcr-Ex.timings

nameusersystemelapsed
amplitudes0.6300.0440.682
basicsSummary0.0070.0000.008
castSummary0.0340.0040.038
classCov0.0940.0150.108
classMeans0.0940.0140.109
classStats0.1200.0200.142
clusterCentres1.3540.0871.448
copiesSummary0.0070.0000.008
ddpcrPlate-class0.4560.0170.476
ddpcrWell-class0.0310.0010.032
ddpcrWell-methods0.4260.0190.453
dropletPlot5.8770.4367.161
exportTable0.2570.0140.445
extractPlateName0.0010.0010.001
extractWellNames0.0010.0000.002
facetPlot3.2860.2064.022
flatPlot5.8670.3516.311
fullCopiesSummary0.0130.0010.015
fullCountsSummary0.0540.0050.059
ggplot.well7.9490.4279.754
gridClassify2.8890.1233.088
heatPlot2.4950.1702.688
kmeansClassify1.4390.1011.557
knnClassify10.236 0.37710.843
mahalanobisRain0.8930.0860.987
mutantCopiesSummary0.0080.0000.008
numDroplets0.5090.0140.527
parseClusterCounts0.0230.0020.025
plateClassification1.6890.0611.779
plateClassificationMethod0.5960.0160.624
plateSummary2.1200.0272.168
positiveCounts0.0350.0010.036
readCSVDataFrame0.0160.0010.018
relabelClasses0.1210.0070.127
removeDropletClasses1.0030.0771.086
renormalisePlate5.6220.2945.965
sdRain3.1830.0943.291
setChannelNames0.0020.0010.002
setDropletVolume0.0000.0000.001
sortDataFrame0.0020.0010.003
sortWells0.4910.0130.505
thresholdClassify2.2030.1042.321
wellClassification0.0390.0020.042
wellClassificationMethod0.0340.0010.036
whiteTheme1.6930.0281.732
wildTypeCopiesSummary0.0090.0010.009