BioC 3.2: CHECK report for flowDensity on oaxaca

Package: flowDensity

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings flowDensity_1.4.0.tar.gz

StartedAt: 2016-04-23 00:08:01 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 00:10:10 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 129.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: flowDensity.Rcheck

Warnings: 2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings flowDensity_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/flowDensity.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.4.0’
* 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 ... [12s/13s] OK
* checking installed package size ... NOTE
  installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc       1.0Mb
    extdata   4.3Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’
A package should be listed in only one of these fields.
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.densityGating’ ‘.ellipseGating’ ‘nmRemove’
* 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 ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'deGate':
deGate
  Code: function(flow.frame, channel, n.sd = 1.5, use.percentile =
                 FALSE, percentile = 0.95, upper = NA, alpha = 0.1,
                 sd.threshold = FALSE, graphs = FALSE, all.cut = FALSE,
                 tinypeak.removal = 1/25, adjust.dens = 1)
  Docs: function(flow.frame, channel, n.sd = 1.5, use.percentile =
                 FALSE, percentile = 0.95, upper = NA, alpha = 0.1,
                 sd.threshold = FALSE, graphs = FALSE, all.cut = FALSE,
                 tinypeak.removal = 1/25)
  Argument names in code not in docs:
    adjust.dens

Codoc mismatches from documentation object 'plotDens':
plotDens
  Code: function(flow.frame, channels, col, main, xlab, ylab, pch =
                 ".", s = FALSE, outdir, file.name, ...)
  Docs: function(flow.frame, channels, col, main, xlab, ylab, pch =
                 ".", s = FALSE, outdir, file.name, devn = TRUE, ...)
  Argument names in docs not in code:
    devn
  Mismatches in argument names:
    Position: 11 Code: ... Docs: devn

* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in documentation object 'deGate':
  ‘adjust.dens’

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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [8s/8s] 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: 2 WARNINGs, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/flowDensity.Rcheck/00check.log’
for details.

* installing *source* package ‘flowDensity’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (flowDensity)

name	user	system	elapsed
CellPopulation-class	0.002	0.001	0.002
deGate	0.373	0.015	0.390
flowDensity	0.365	0.010	0.375
getflowFrame	0.336	0.014	0.350
nmRemove	0.202	0.012	0.220
notSubFrame	0.096	0.009	0.107
plotDens	0.340	0.013	0.361