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This page was generated on 2023-06-06 11:00:44 -0000 (Tue, 06 Jun 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.0 (2023-04-21) -- "Already Tomorrow" 4366
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 kunpeng2


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 2129/2199HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
twoddpcr 1.25.0  (landing page)
Anthony Chiu
Snapshot Date: 2023-06-05 06:35:06 -0000 (Mon, 05 Jun 2023)
git_url: https://git.bioconductor.org/packages/twoddpcr
git_branch: devel
git_last_commit: 44bca1b
git_last_commit_date: 2023-04-25 14:52:34 -0000 (Tue, 25 Apr 2023)
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

Summary

Package: twoddpcr
Version: 1.25.0
Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:twoddpcr.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings twoddpcr_1.25.0.tar.gz
StartedAt: 2023-06-06 09:03:32 -0000 (Tue, 06 Jun 2023)
EndedAt: 2023-06-06 09:09:19 -0000 (Tue, 06 Jun 2023)
EllapsedTime: 347.5 seconds
RetCode: 0
Status:   OK  
CheckDir: twoddpcr.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:twoddpcr.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings twoddpcr_1.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/twoddpcr.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘twoddpcr/DESCRIPTION’ ... OK
* this is package ‘twoddpcr’ version ‘1.25.0’
* 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 ... NOTE
S3 methods shown with full name in documentation object 'ggplot.well':
  ‘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 17.657  0.060  17.741
ggplot.well  5.719  0.091   5.818
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/twoddpcr.Rcheck/00check.log’
for details.



Installation output

twoddpcr.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL twoddpcr
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.0/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 version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 
  7.786   0.220   8.008 

Example timings

twoddpcr.Rcheck/twoddpcr-Ex.timings

nameusersystemelapsed
amplitudes0.4230.0040.427
basicsSummary0.0060.0000.007
castSummary0.0240.0000.023
classCov0.0750.0000.075
classMeans0.0750.0110.085
classStats0.1010.0000.101
clusterCentres0.9360.0000.938
copiesSummary0.0070.0000.007
ddpcrPlate-class0.3240.0040.329
ddpcrWell-class0.0270.0000.028
ddpcrWell-methods0.3030.0000.303
dropletPlot4.2440.4084.657
exportTable0.1770.0160.195
extractPlateName000
extractWellNames000
facetPlot2.3560.0602.419
flatPlot4.4340.0794.519
fullCopiesSummary0.0090.0010.010
fullCountsSummary0.0340.0040.038
ggplot.well5.7190.0915.818
gridClassify4.3920.0524.450
heatPlot1.7540.0281.784
kmeansClassify1.5240.0081.534
knnClassify17.657 0.06017.741
mahalanobisRain1.2710.0321.303
mutantCopiesSummary0.0050.0000.005
numDroplets0.3080.0000.309
parseClusterCounts0.0150.0000.016
plateClassification1.3080.0081.319
plateClassificationMethod0.640.000.64
plateSummary1.9980.0002.000
positiveCounts0.0300.0000.029
readCSVDataFrame0.0150.0000.015
relabelClasses0.1000.0000.099
removeDropletClasses1.0620.0001.063
renormalisePlate4.0660.0124.083
sdRain3.3110.0123.325
setChannelNames0.0020.0000.002
setDropletVolume0.0000.0000.001
sortDataFrame0.0030.0000.003
sortWells0.3130.0160.329
thresholdClassify1.9930.0162.011
wellClassification0.0170.0040.021
wellClassificationMethod0.0230.0000.023
whiteTheme1.1310.0121.144
wildTypeCopiesSummary0.0050.0000.005