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CHECK report for flowDensity on malbec1

This page was generated on 2020-04-15 12:08:50 -0400 (Wed, 15 Apr 2020).

Package 588/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowDensity 1.20.0
Mehrnoush Malek
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/flowDensity
Branch: RELEASE_3_10
Last Commit: 4adae8e
Last Changed Date: 2019-10-29 13:09:00 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: flowDensity
Version: 1.20.0
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:flowDensity.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings flowDensity_1.20.0.tar.gz
StartedAt: 2020-04-15 02:18:12 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 02:19:52 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 99.3 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: flowDensity.Rcheck
Warnings: 5

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:flowDensity.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings flowDensity_1.20.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/flowDensity.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.20.0’
* 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: bad markup (extra space?) at plotDens.Rd:62:19
  Warning: replacing previous import ‘flowCore::plot’ by ‘graphics::plot’ when loading ‘flowDensity’
See ‘/home/biocbuild/bbs-3.10-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 ... WARNING
prepare_Rd: bad markup (extra space?) at plotDens.Rd:62:19
* 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: 5 WARNINGs
See
  ‘/home/biocbuild/bbs-3.10-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-3.10-bioc/R/bin/R CMD INSTALL flowDensity
###
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* installing to library ‘/home/biocbuild/bbs-3.10-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
Warning: bad markup (extra space?) at plotDens.Rd:62:19
*** 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-class0.0000.0000.001
deGate0.2120.0240.299
flowDensity0.0760.0000.079
getPeaks0.0320.0000.033
getflowFrame0.0720.0000.075
nmRemove0.2640.0040.288
notSubFrame0.1160.0000.117
plotDens0.1440.0080.151