Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:08:00 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 flowDensity on machv2


To the developers/maintainers of the flowDensity package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/flowDensity.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 660/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowDensity 1.28.0  (landing page)
Mehrnoush Malek
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/flowDensity
git_branch: RELEASE_3_14
git_last_commit: 26bbabf
git_last_commit_date: 2021-10-26 12:14:21 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: flowDensity
Version: 1.28.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:flowDensity.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings flowDensity_1.28.0.tar.gz
StartedAt: 2022-04-12 13:22:10 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 13:24:46 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 156.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: flowDensity.Rcheck
Warnings: 4

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:flowDensity.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings flowDensity_1.28.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/flowDensity.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowDensity/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowDensity’ version ‘1.28.0’
* 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 ‘flowDensity’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘flowCore::plot’ by ‘graphics::plot’ when loading ‘flowDensity’
See ‘/Users/biocbuild/bbs-3.14-bioc/meat/flowDensity.Rcheck/00install.out’ for details.
* 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 ... WARNING
Rd files with duplicated alias 'flowDensity':
  ‘flowDensity-methods.Rd’ ‘flowDensity.Rd’
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic 'flowDensity' and siglist
    'CellPopulation,ANY,logical,missing'
  generic 'flowDensity' and siglist 'GatingHierarchy,ANY,logical,ANY'
  generic 'flowDensity' and siglist 'flowFrame,ANY,logical,missing'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Objects in \usage without \alias in documentation object 'flowDensity-methods':
  ‘\S4method{flowDensity}{CellPopulation,ANY,logical,missing}’
  ‘\S4method{flowDensity}{flowFrame,ANY,logical,missing}’
  ‘\S4method{flowDensity}{GatingHierarchy,ANY,logical,ANY}’

Undocumented arguments in documentation object 'plotDens'
  ‘dens.col’ ‘cex’ ‘dens.type’
Documented arguments not in \usage in documentation object 'plotDens':
  ‘density.type’ ‘density.col’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: 4 WARNINGs
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/flowDensity.Rcheck/00check.log’
for details.



Installation output

flowDensity.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL flowDensity
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘flowDensity’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘flowCore::plot’ by ‘graphics::plot’ when loading ‘flowDensity’
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘flowDensity.Rmd’ 
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘flowCore::plot’ by ‘graphics::plot’ when loading ‘flowDensity’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘flowCore::plot’ by ‘graphics::plot’ when loading ‘flowDensity’
** testing if installed package keeps a record of temporary installation path
* DONE (flowDensity)

Tests output


Example timings

flowDensity.Rcheck/flowDensity-Ex.timings

nameusersystemelapsed
CellPopulation-class0.0020.0010.003
deGate0.2090.0280.237
flowDensity0.1010.0090.111
getPeaks0.0370.0040.040
getflowFrame0.1690.0110.179
nmRemove0.2860.0240.311
notSubFrame0.4400.0120.454
plotDens0.1780.0280.207