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This page was generated on 2025-10-16 12:05 -0400 (Thu, 16 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4867
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4655
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4600
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4610
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 2267/2346HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
twoddpcr 1.33.0  (landing page)
Anthony Chiu
Snapshot Date: 2025-10-15 13:45 -0400 (Wed, 15 Oct 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 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for twoddpcr on lconway

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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:twoddpcr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings twoddpcr_1.33.0.tar.gz
StartedAt: 2025-10-16 02:11:45 -0400 (Thu, 16 Oct 2025)
EndedAt: 2025-10-16 02:14:14 -0400 (Thu, 16 Oct 2025)
EllapsedTime: 148.4 seconds
RetCode: 0
Status:   OK  
CheckDir: twoddpcr.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:twoddpcr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings twoddpcr_1.33.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/twoddpcr.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 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  8.685  0.220   9.002
ggplot.well  6.122  0.282   6.477
gridClassify 5.326  0.173   5.538
dropletPlot  5.045  0.215   5.306
* 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 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-3.22-bioc/meat/twoddpcr.Rcheck/00check.log’
for details.


Installation output

twoddpcr.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 2 | SKIP 0 | PASS 155 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 155 ]
> 
> proc.time()
   user  system elapsed 
  7.706   0.569   8.362 

Example timings

twoddpcr.Rcheck/twoddpcr-Ex.timings

nameusersystemelapsed
amplitudes0.3250.0260.355
basicsSummary0.0050.0010.006
castSummary0.0180.0050.022
classCov0.0640.0110.075
classMeans0.0660.0160.084
classStats0.0710.0080.081
clusterCentres0.8330.0740.915
copiesSummary0.0070.0010.008
ddpcrPlate-class0.3170.0120.333
ddpcrWell-class0.0490.0090.058
ddpcrWell-methods0.2700.0110.283
dropletPlot5.0450.2155.306
exportTable0.1530.0260.197
extractPlateName0.0000.0000.001
extractWellNames0.0010.0000.000
facetPlot2.5160.0872.617
flatPlot4.2350.2534.557
fullCopiesSummary0.0060.0020.008
fullCountsSummary0.0260.0070.033
ggplot.well6.1220.2826.477
gridClassify5.3260.1735.538
heatPlot1.7630.0641.842
kmeansClassify1.1090.0631.181
knnClassify8.6850.2209.002
mahalanobisRain0.6650.0530.724
mutantCopiesSummary0.0050.0010.006
numDroplets0.2720.0130.288
parseClusterCounts0.0090.0020.010
plateClassification1.1400.0311.183
plateClassificationMethod0.3980.0110.411
plateSummary1.6480.0221.697
positiveCounts0.0300.0010.030
readCSVDataFrame0.0140.0040.019
relabelClasses0.0920.0050.098
removeDropletClasses0.6780.0480.748
renormalisePlate3.2650.2113.527
sdRain2.3800.0452.445
setChannelNames0.0020.0020.003
setDropletVolume0.0000.0010.001
sortDataFrame0.0030.0010.004
sortWells0.2790.0020.282
thresholdClassify1.7040.0601.782
wellClassification0.0210.0010.022
wellClassificationMethod0.0220.0000.023
whiteTheme1.5830.0471.641
wildTypeCopiesSummary0.0030.0020.004