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This page was generated on 2021-10-15 15:05:55 -0400 (Fri, 15 Oct 2021).

CHECK results for twoddpcr on nebbiolo1

To the developers/maintainers of the twoddpcr package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/twoddpcr.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1979/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
twoddpcr 1.16.0  (landing page)
Anthony Chiu
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/twoddpcr
git_branch: RELEASE_3_13
git_last_commit: c997928
git_last_commit_date: 2021-05-19 12:26:06 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: twoddpcr
Version: 1.16.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:twoddpcr.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings twoddpcr_1.16.0.tar.gz
StartedAt: 2021-10-14 11:58:23 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 12:00:35 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 132.4 seconds
RetCode: 0
Status:   OK  
CheckDir: twoddpcr.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:twoddpcr.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings twoddpcr_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/twoddpcr.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘twoddpcr/DESCRIPTION’ ... OK
* this is package ‘twoddpcr’ version ‘1.16.0’
* 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 LazyData ... 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
ggplot.well  7.425  0.164   7.591
knnClassify  7.144  0.028   7.172
gridClassify 4.752  0.288   5.040
* 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:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL twoddpcr
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 155 ]
> 
> proc.time()
   user  system elapsed 
  5.839   0.248   6.073 

Example timings

twoddpcr.Rcheck/twoddpcr-Ex.timings

nameusersystemelapsed
amplitudes0.3360.0320.368
basicsSummary0.0030.0040.007
castSummary0.0090.0110.021
classCov0.0600.0050.064
classMeans0.0550.0000.055
classStats0.0640.0040.068
clusterCentres0.8510.0030.856
copiesSummary0.0070.0000.007
ddpcrPlate-class0.2930.0000.293
ddpcrWell-class0.0240.0000.024
ddpcrWell-methods0.2850.0000.285
dropletPlot4.2910.0684.359
exportTable0.1300.0060.136
extractPlateName0.0010.0000.000
extractWellNames0.0000.0000.001
facetPlot1.8720.0321.904
flatPlot4.4540.0764.532
fullCopiesSummary0.0040.0040.008
fullCountsSummary0.0310.0080.039
ggplot.well7.4250.1647.591
gridClassify4.7520.2885.040
heatPlot1.5170.0561.573
kmeansClassify1.0140.0361.050
knnClassify7.1440.0287.172
mahalanobisRain0.6250.0040.628
mutantCopiesSummary0.0000.0040.005
numDroplets0.2700.0030.272
parseClusterCounts0.0050.0080.013
plateClassification1.0850.0081.093
plateClassificationMethod0.3920.0000.391
plateSummary2.2120.0002.212
positiveCounts0.0550.0000.055
readCSVDataFrame0.0120.0000.013
relabelClasses0.0430.0000.043
removeDropletClasses0.6260.0000.626
renormalisePlate3.4370.0003.438
sdRain3.2330.0073.241
setChannelNames0.0010.0000.002
setDropletVolume0.0000.0000.001
sortDataFrame0.0000.0020.003
sortWells0.2750.0010.276
thresholdClassify1.8360.0081.843
wellClassification0.0140.0040.017
wellClassificationMethod0.020.000.02
whiteTheme1.3540.0121.367
wildTypeCopiesSummary0.0050.0000.005