Back to Multiple platform build/check report for BioC 3.17
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This page was generated on 2023-04-12 10:55:43 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_644.3.0 alpha (2023-04-03 r84154) 4547
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_64R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" 4333
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

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.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 2137/2207HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
twoddpcr 1.23.0  (landing page)
Anthony Chiu
Snapshot Date: 2023-04-11 14:00:16 -0400 (Tue, 11 Apr 2023)
git_url: https://git.bioconductor.org/packages/twoddpcr
git_branch: devel
git_last_commit: 2c97ec8
git_last_commit_date: 2022-11-01 11:15:14 -0400 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  

Summary

Package: twoddpcr
Version: 1.23.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:twoddpcr.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings twoddpcr_1.23.0.tar.gz
StartedAt: 2023-04-12 10:04:44 -0400 (Wed, 12 Apr 2023)
EndedAt: 2023-04-12 10:08:54 -0400 (Wed, 12 Apr 2023)
EllapsedTime: 250.7 seconds
RetCode: 0
Status:   OK  
CheckDir: twoddpcr.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:twoddpcr.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings twoddpcr_1.23.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/twoddpcr.Rcheck’
* using R Under development (unstable) (2023-02-14 r83833)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
    GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
* running under: Ubuntu 20.04.6 LTS
* using session charset: UTF-8
* checking for file ‘twoddpcr/DESCRIPTION’ ... OK
* this is package ‘twoddpcr’ version ‘1.23.0’
* 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 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 ... 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  7.843  0.060   7.905
ggplot.well  6.839  0.136   6.975
gridClassify 5.127  0.116   5.244
* 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 ...
  ‘twoddpcr.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

twoddpcr.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL twoddpcr
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-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 Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences"
Copyright (C) 2023 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 2 | SKIP 0 | PASS 155 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 155 ]
> 
> proc.time()
   user  system elapsed 
  5.811   0.226   6.019 

Example timings

twoddpcr.Rcheck/twoddpcr-Ex.timings

nameusersystemelapsed
amplitudes0.3730.0210.392
basicsSummary0.0050.0000.005
castSummary0.0180.0000.017
classCov0.0460.0040.050
classMeans0.0620.0000.062
classStats0.0680.0000.067
clusterCentres0.8060.0110.818
copiesSummary0.0050.0010.005
ddpcrPlate-class0.3230.0030.329
ddpcrWell-class0.0310.0000.032
ddpcrWell-methods0.4680.0000.468
dropletPlot4.2740.0914.366
exportTable0.1450.0100.156
extractPlateName0.0010.0000.000
extractWellNames0.0010.0000.000
facetPlot2.1010.0882.189
flatPlot4.5610.0844.645
fullCopiesSummary0.0050.0000.005
fullCountsSummary0.0230.0000.023
ggplot.well6.8390.1366.975
gridClassify5.1270.1165.244
heatPlot1.6330.0121.645
kmeansClassify0.9940.0081.002
knnClassify7.8430.0607.905
mahalanobisRain0.6880.0000.687
mutantCopiesSummary0.0040.0000.003
numDroplets0.2910.0000.292
parseClusterCounts0.0110.0000.011
plateClassification1.0410.0081.049
plateClassificationMethod0.3830.0000.383
plateSummary2.3480.0082.357
positiveCounts0.0260.0000.026
readCSVDataFrame0.0460.0000.046
relabelClasses0.3030.0000.303
removeDropletClasses0.5470.0040.552
renormalisePlate2.7930.0122.805
sdRain3.2880.0523.340
setChannelNames0.0010.0000.001
setDropletVolume000
sortDataFrame0.0020.0000.002
sortWells0.2740.0040.277
thresholdClassify1.7690.0361.804
wellClassification0.0130.0050.017
wellClassificationMethod0.0270.0020.030
whiteTheme1.4880.0081.496
wildTypeCopiesSummary0.0030.0000.003