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This page was generated on 2021-10-22 12:04:00 -0400 (Fri, 22 Oct 2021).

CHECK results for flowDensity on nebbiolo2

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? here 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 656/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowDensity 1.27.2  (landing page)
Mehrnoush Malek
Snapshot Date: 2021-10-21 14:50:08 -0400 (Thu, 21 Oct 2021)
git_url: https://git.bioconductor.org/packages/flowDensity
git_branch: master
git_last_commit: 47fb2ff8
git_last_commit_date: 2021-08-06 12:18:05 -0400 (Fri, 06 Aug 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    NA  

Summary

Package: flowDensity
Version: 1.27.2
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:flowDensity.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings flowDensity_1.27.2.tar.gz
StartedAt: 2021-10-21 20:07:58 -0400 (Thu, 21 Oct 2021)
EndedAt: 2021-10-21 20:09:26 -0400 (Thu, 21 Oct 2021)
EllapsedTime: 87.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: flowDensity.Rcheck
Warnings: 4

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:flowDensity.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings flowDensity_1.27.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/flowDensity.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (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 ‘1.27.2’
* 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 ‘/home/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
  ‘/home/biocbuild/bbs-3.14-bioc/meat/flowDensity.Rcheck/00check.log’
for details.



Installation output

flowDensity.Rcheck/00install.out

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### Running command:
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###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL flowDensity
###
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/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-class0.0010.0000.001
deGate0.1320.0160.148
flowDensity0.0640.0000.064
getPeaks0.0220.0000.022
getflowFrame0.0450.0040.049
nmRemove0.2400.0080.249
notSubFrame0.0870.0040.091
plotDens0.4160.0040.420