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This page was generated on 2025-08-09 12:06 -0400 (Sat, 09 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4553
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 2238/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
twoddpcr 1.33.0  (landing page)
Anthony Chiu
Snapshot Date: 2025-08-08 13:45 -0400 (Fri, 08 Aug 2025)
git_url: https://git.bioconductor.org/packages/twoddpcr
git_branch: devel
git_last_commit: 5db39f4
git_last_commit_date: 2025-04-15 11:08:59 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for twoddpcr on nebbiolo2

To the developers/maintainers of the twoddpcr package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: twoddpcr
Version: 1.33.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:twoddpcr.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings twoddpcr_1.33.0.tar.gz
StartedAt: 2025-08-09 03:45:47 -0400 (Sat, 09 Aug 2025)
EndedAt: 2025-08-09 03:49:50 -0400 (Sat, 09 Aug 2025)
EllapsedTime: 243.3 seconds
RetCode: 0
Status:   OK  
CheckDir: twoddpcr.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:twoddpcr.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings twoddpcr_1.33.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/twoddpcr.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘twoddpcr/DESCRIPTION’ ... OK
* this is package ‘twoddpcr’ version ‘1.33.0’
* 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 code 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 ... NOTE
S3 methods shown with full name in Rd file 'ggplot.well.Rd':
  ‘ggplot.well’ ‘ggplot.plate’

The \usage entries for S3 methods should use the \method markup and not
their full name.
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 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 6.914  0.041   6.955
ggplot.well 6.267  0.136   6.403
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/twoddpcr.Rcheck/00check.log’
for details.


Installation output

twoddpcr.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL twoddpcr
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘twoddpcr’ ...
** this is package ‘twoddpcr’ version ‘1.33.0’
** 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 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 3 | SKIP 0 | PASS 155 ]

[ FAIL 0 | WARN 3 | SKIP 0 | PASS 155 ]
> 
> proc.time()
   user  system elapsed 
  5.661   0.281   5.934 

Example timings

twoddpcr.Rcheck/twoddpcr-Ex.timings

nameusersystemelapsed
amplitudes0.2490.0260.275
basicsSummary0.0040.0000.004
castSummary0.0130.0010.014
classCov0.0490.0110.060
classMeans0.0530.0000.053
classStats0.0730.0040.077
clusterCentres0.5660.0140.580
copiesSummary0.0040.0010.005
ddpcrPlate-class0.3450.0100.355
ddpcrWell-class0.0160.0000.016
ddpcrWell-methods0.1640.0000.165
dropletPlot3.7850.0583.844
exportTable0.1270.0030.131
extractPlateName000
extractWellNames0.0010.0000.001
facetPlot1.810.061.87
flatPlot3.8810.0523.933
fullCopiesSummary0.0050.0010.005
fullCountsSummary0.0220.0000.022
ggplot.well6.2670.1366.403
gridClassify4.4750.0494.525
heatPlot1.1830.0061.189
kmeansClassify0.8620.0020.864
knnClassify6.9140.0416.955
mahalanobisRain0.5970.0050.603
mutantCopiesSummary0.0030.0010.004
numDroplets0.3820.0090.391
parseClusterCounts0.0100.0000.011
plateClassification0.7840.0060.790
plateClassificationMethod0.2800.0030.284
plateSummary1.7180.0001.717
positiveCounts0.0230.0010.024
readCSVDataFrame0.0110.0000.012
relabelClasses0.0440.0000.044
removeDropletClasses0.6340.0020.636
renormalisePlate2.8090.0082.817
sdRain2.9770.0012.978
setChannelNames0.0010.0000.001
setDropletVolume0.0010.0000.000
sortDataFrame0.0000.0000.001
sortWells0.1560.0000.156
thresholdClassify1.1150.0471.162
wellClassification0.0140.0000.014
wellClassificationMethod0.0140.0000.015
whiteTheme1.3260.0161.342
wildTypeCopiesSummary0.0030.0000.003