Package: flowDensity

Version: 1.20.0

Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowDensity.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings flowDensity_1.20.0.tar.gz

StartedAt: 2020-04-15 03:13:16 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 03:15:21 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 125.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: flowDensity.Rcheck

Warnings: 5

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### Running command:
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###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowDensity.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings flowDensity_1.20.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/flowDensity.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '1.20.0'
* 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 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-3.10-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
* 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-3.10-bioc/meat/flowDensity.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/flowDensity_1.20.0.tar.gz && rm -rf flowDensity.buildbin-libdir && mkdir flowDensity.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowDensity.buildbin-libdir flowDensity_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL flowDensity_1.20.0.zip && rm flowDensity_1.20.0.tar.gz flowDensity_1.20.0.zip
###
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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_1.20.0.zip
* DONE (flowDensity)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'flowDensity' successfully unpacked and MD5 sums checked