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CHECK report for flowDensity on tokay2

This page was generated on 2020-10-17 11:56:35 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE flowDensity PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 612/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowDensity 1.22.0
Mehrnoush Malek
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/flowDensity
Branch: RELEASE_3_11
Last Commit: e9c887a
Last Changed Date: 2020-04-27 14:41:18 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: flowDensity
Version: 1.22.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowDensity.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings flowDensity_1.22.0.tar.gz
StartedAt: 2020-10-17 04:06:35 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 04:09:30 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 174.9 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: flowDensity.Rcheck
Warnings: 5

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowDensity.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings flowDensity_1.22.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/flowDensity.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'flowDensity/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowDensity' version '1.22.0'
* 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 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 'C:/Users/biocbuild/bbs-3.11-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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/flowDensity.Rcheck/00check.log'
for details.



Installation output

flowDensity.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/flowDensity_1.22.0.tar.gz && rm -rf flowDensity.buildbin-libdir && mkdir flowDensity.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowDensity.buildbin-libdir flowDensity_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL flowDensity_1.22.0.zip && rm flowDensity_1.22.0.tar.gz flowDensity_1.22.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 4398k  100 4398k    0     0  46.0M      0 --:--:-- --:--:-- --:--:-- 49.3M

install for i386

* 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
  converting help for package 'flowDensity'
    finding HTML links ... done
    CellPopulation-class                    html  
    deGate                                  html  
    flowDensity-methods                     html  
    flowDensity                             html  
    getPeaks                                html  
    getflowFrame                            html  
    nmRemove                                html  
    notSubFrame                             html  
    plotDens                                html  
** 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

install for x64

* installing *source* package 'flowDensity' ...
** testing if installed package can be loaded
Warning: replacing previous import 'flowCore::plot' by 'graphics::plot' when loading 'flowDensity'
* MD5 sums
packaged installation of 'flowDensity' as flowDensity_1.22.0.zip
* DONE (flowDensity)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'flowDensity' successfully unpacked and MD5 sums checked

Tests output


Example timings

flowDensity.Rcheck/examples_i386/flowDensity-Ex.timings

nameusersystemelapsed
CellPopulation-class000
deGate0.290.030.46
flowDensity0.110.000.11
getPeaks0.050.000.05
getflowFrame0.230.020.25
nmRemove0.340.000.53
notSubFrame0.190.000.26
plotDens0.270.000.27

flowDensity.Rcheck/examples_x64/flowDensity-Ex.timings

nameusersystemelapsed
CellPopulation-class000
deGate0.220.000.22
flowDensity0.110.020.13
getPeaks0.010.000.01
getflowFrame0.070.000.06
nmRemove0.230.010.25
notSubFrame0.160.020.71
plotDens0.290.000.30