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This page was generated on 2024-04-29 11:41:32 -0400 (Mon, 29 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4752
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4518
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4475
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 2226/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
twoddpcr 1.27.0  (landing page)
Anthony Chiu
Snapshot Date: 2024-04-28 14:00:16 -0400 (Sun, 28 Apr 2024)
git_url: https://git.bioconductor.org/packages/twoddpcr
git_branch: devel
git_last_commit: f5cb7f9
git_last_commit_date: 2023-10-24 10:55:41 -0400 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows 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
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

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.
- 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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: twoddpcr
Version: 1.27.0
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:twoddpcr.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings twoddpcr_1.27.0.tar.gz
StartedAt: 2024-04-29 11:37:02 -0000 (Mon, 29 Apr 2024)
EndedAt: 2024-04-29 11:39:32 -0000 (Mon, 29 Apr 2024)
EllapsedTime: 150.4 seconds
RetCode: 0
Status:   OK  
CheckDir: twoddpcr.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:twoddpcr.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings twoddpcr_1.27.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/twoddpcr.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* 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
* using option ‘--no-vignettes’
* checking for file ‘twoddpcr/DESCRIPTION’ ... OK
* this is package ‘twoddpcr’ version ‘1.27.0’
* 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 18.314  0.072  18.406
ggplot.well  5.665  0.103   5.781
* 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
  ‘/home/biocbuild/bbs-3.19-bioc/meat/twoddpcr.Rcheck/00check.log’
for details.


Installation output

twoddpcr.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL twoddpcr
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/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 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 
  8.233   0.267   8.505 

Example timings

twoddpcr.Rcheck/twoddpcr-Ex.timings

nameusersystemelapsed
amplitudes0.3920.0160.408
basicsSummary0.0060.0000.006
castSummary0.0210.0000.022
classCov0.0740.0120.086
classMeans0.0760.0000.075
classStats0.10.00.1
clusterCentres1.0120.0081.022
copiesSummary0.0060.0000.006
ddpcrPlate-class0.3330.0000.336
ddpcrWell-class0.0300.0000.031
ddpcrWell-methods0.3450.0000.346
dropletPlot4.2230.0764.307
exportTable0.1900.0000.193
extractPlateName0.0000.0000.001
extractWellNames0.0010.0000.001
facetPlot2.5040.0562.565
flatPlot4.2840.0644.355
fullCopiesSummary0.0080.0000.008
fullCountsSummary0.0350.0000.036
ggplot.well5.6650.1035.781
gridClassify4.3660.0604.433
heatPlot1.9010.0241.932
kmeansClassify1.4640.0041.471
knnClassify18.314 0.07218.406
mahalanobisRain1.1470.0311.180
mutantCopiesSummary0.0060.0000.005
numDroplets0.3460.0040.350
parseClusterCounts0.0110.0040.016
plateClassification1.7360.0041.744
plateClassificationMethod0.4430.0000.444
plateSummary2.0890.0042.097
positiveCounts0.0320.0000.032
readCSVDataFrame0.0150.0000.015
relabelClasses0.0590.0000.059
removeDropletClasses1.0300.0081.040
renormalisePlate4.8030.0244.837
sdRain3.6460.0003.655
setChannelNames0.0010.0000.002
setDropletVolume0.0000.0000.001
sortDataFrame0.0020.0000.003
sortWells0.3020.0000.303
thresholdClassify2.2480.0362.290
wellClassification0.0250.0000.025
wellClassificationMethod0.0250.0000.024
whiteTheme1.1040.0161.122
wildTypeCopiesSummary0.0060.0000.005