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This page was generated on 2021-10-15 15:06:57 -0400 (Fri, 15 Oct 2021).

CHECK results for twoddpcr on machv2

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: /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_1.16.0.tar.gz
StartedAt: 2021-10-15 01:02:15 -0400 (Fri, 15 Oct 2021)
EndedAt: 2021-10-15 01:04:52 -0400 (Fri, 15 Oct 2021)
EllapsedTime: 157.2 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_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/twoddpcr.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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
knnClassify  9.778  0.146   9.941
ggplot.well  6.819  0.248   7.078
gridClassify 6.129  0.131   6.272
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/twoddpcr.Rcheck/00check.log’
for details.



Installation output

twoddpcr.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 155 ]
> 
> proc.time()
   user  system elapsed 
  8.140   0.416   8.546 

Example timings

twoddpcr.Rcheck/twoddpcr-Ex.timings

nameusersystemelapsed
amplitudes0.4860.0310.517
basicsSummary0.0100.0010.011
castSummary0.0260.0050.031
classCov0.0660.0100.076
classMeans0.0640.0080.072
classStats0.0760.0180.094
clusterCentres0.8320.0490.881
copiesSummary0.0060.0010.008
ddpcrPlate-class0.3930.0130.406
ddpcrWell-class0.0290.0010.030
ddpcrWell-methods0.3520.0110.363
dropletPlot4.0540.1904.266
exportTable0.2060.0140.222
extractPlateName0.0000.0000.001
extractWellNames0.0010.0010.001
facetPlot2.5230.0732.602
flatPlot4.6480.1754.833
fullCopiesSummary0.0120.0020.015
fullCountsSummary0.0400.0080.048
ggplot.well6.8190.2487.078
gridClassify6.1290.1316.272
heatPlot1.9670.0562.026
kmeansClassify1.3880.0491.439
knnClassify9.7780.1469.941
mahalanobisRain0.8650.0240.889
mutantCopiesSummary0.0070.0010.007
numDroplets0.3680.0050.374
parseClusterCounts0.0180.0020.020
plateClassification1.3940.0201.415
plateClassificationMethod0.5390.0050.545
plateSummary2.1280.0062.137
positiveCounts0.0340.0010.034
readCSVDataFrame0.0150.0030.018
relabelClasses0.1200.0020.122
removeDropletClasses0.8840.0230.911
renormalisePlate4.0920.1284.223
sdRain2.8010.0322.835
setChannelNames0.0010.0010.002
setDropletVolume0.0000.0000.001
sortDataFrame0.0020.0010.003
sortWells0.2980.0070.305
thresholdClassify1.9460.0251.973
wellClassification0.0230.0010.024
wellClassificationMethod0.0250.0010.025
whiteTheme1.6150.0401.665
wildTypeCopiesSummary0.0070.0020.009