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This page was generated on 2023-10-20 09:38:14 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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 2160/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
twoddpcr 1.24.0  (landing page)
Anthony Chiu
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/twoddpcr
git_branch: RELEASE_3_17
git_last_commit: 2f098ed
git_last_commit_date: 2023-04-25 10:52:34 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for twoddpcr on kjohnson2


To the developers/maintainers of the twoddpcr package:
- 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: 1.24.0
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_1.24.0.tar.gz
StartedAt: 2023-10-19 08:47:45 -0400 (Thu, 19 Oct 2023)
EndedAt: 2023-10-19 08:52:02 -0400 (Thu, 19 Oct 2023)
EllapsedTime: 256.9 seconds
RetCode: 0
Status:   OK  
CheckDir: twoddpcr.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/twoddpcr.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘twoddpcr/DESCRIPTION’ ... OK
* this is package ‘twoddpcr’ version ‘1.24.0’
* 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 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      8.574  0.158  14.102
ggplot.well      7.049  0.208  12.805
gridClassify     5.948  0.109  10.335
dropletPlot      4.380  0.174   8.082
renormalisePlate 3.969  0.054   7.123
flatPlot         3.727  0.175   6.997
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/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/4.3-arm64/Resources/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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 
  7.033   0.365  13.255 

Example timings

twoddpcr.Rcheck/twoddpcr-Ex.timings

nameusersystemelapsed
amplitudes0.3780.0210.715
basicsSummary0.0060.0010.013
castSummary0.0180.0040.039
classCov0.0600.0040.117
classMeans0.2000.0090.372
classStats0.0730.0070.147
clusterCentres0.7670.0251.419
copiesSummary0.0060.0010.015
ddpcrPlate-class0.2930.0080.533
ddpcrWell-class0.0250.0010.049
ddpcrWell-methods0.2750.0050.499
dropletPlot4.3800.1748.082
exportTable0.1730.0230.388
extractPlateName0.0010.0010.001
extractWellNames0.0010.0010.005
facetPlot2.4730.0654.554
flatPlot3.7270.1756.997
fullCopiesSummary0.0070.0020.015
fullCountsSummary0.0310.0060.068
ggplot.well 7.049 0.20812.805
gridClassify 5.948 0.10910.335
heatPlot1.7710.0423.196
kmeansClassify1.1610.0271.957
knnClassify 8.574 0.15814.102
mahalanobisRain0.7660.0131.356
mutantCopiesSummary0.0050.0010.010
numDroplets0.3060.0030.556
parseClusterCounts0.0140.0030.033
plateClassification1.2150.0212.212
plateClassificationMethod0.3990.0050.727
plateSummary1.7000.0173.069
positiveCounts0.0260.0010.048
readCSVDataFrame0.0160.0040.038
relabelClasses0.1180.0050.221
removeDropletClasses0.7110.0161.298
renormalisePlate3.9690.0547.123
sdRain2.4690.0244.460
setChannelNames0.0010.0000.002
setDropletVolume0.0000.0000.001
sortDataFrame0.0020.0010.003
sortWells0.3530.0040.636
thresholdClassify1.8200.0273.298
wellClassification0.0590.0060.114
wellClassificationMethod0.0260.0010.045
whiteTheme1.7170.0373.130
wildTypeCopiesSummary0.0280.0020.055