Package: flowDensity

Version: 1.14.0

Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:flowDensity.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings flowDensity_1.14.0.tar.gz

StartedAt: 2018-10-16 00:25:16 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 00:26:27 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 71.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: flowDensity.Rcheck

Warnings: 5

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:flowDensity.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings flowDensity_1.14.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/flowDensity.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.14.0’
* 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 ‘/home/biocbuild/bbs-3.7-bioc/meat/flowDensity.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc       2.7Mb
    extdata   4.3Mb
* 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}’

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’ ... WARNING
Vignette sources in 'inst/doc' missing from the 'vignettes' directory:
  ‘flowDensity.Rnw’
* 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, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.7-bioc/meat/flowDensity.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL flowDensity
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘flowDensity’ ...
** 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
   ‘flowDensityVignette.Rnw’ 
** testing if installed package can be loaded
Warning: replacing previous import ‘flowCore::plot’ by ‘graphics::plot’ when loading ‘flowDensity’
* DONE (flowDensity)

name	user	system	elapsed
CellPopulation-class	0.000	0.000	0.002
deGate	0.148	0.008	0.206
flowDensity	0.056	0.004	0.060
getPeaks	0.024	0.000	0.026
getflowFrame	0.048	0.000	0.050
nmRemove	0.172	0.004	0.177
notSubFrame	0.124	0.000	0.139
plotDens	0.116	0.008	0.123