Package: flowDensity

Version: 1.12.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings flowDensity_1.12.0.tar.gz

StartedAt: 2018-04-12 03:45:33 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 03:47:19 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 105.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: flowDensity.Rcheck

Warnings: 4

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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_1.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/flowDensity.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.12.0’
* 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 ... OK
* checking installed package size ... NOTE
  installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc       1.4Mb
    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 ... NOTE
.deGate2D: no visible global function definition for ‘chull’
.deGatePlot: no visible global function definition for ‘par’
.deGatePlot: no visible global function definition for ‘polygon’
.deGatePlot: no visible global function definition for ‘abline’
.deGatePlot: no visible global function definition for ‘colors’
.deGatePlot: no visible global function definition for ‘mtext’
.densityForPlot: no visible global function definition for ‘density’
.densityForPlot: no visible global function definition for
  ‘smooth.spline’
.densityGating: no visible global function definition for ‘sd’
.densityGating: no visible global function definition for ‘median’
.densityGating: no visible global function definition for ‘quantile’
.flowDensity.2d: no visible binding for global variable
  ‘remove.margins’
.flowDensity.2d: no visible global function definition for ‘chull’
.getFlex: no visible binding for global variable ‘magnitude’
.getIntersect: no visible global function definition for ‘splinefun’
.getScoreIndex: no visible global function definition for ‘splinefun’
.getScoreIndex: no visible global function definition for ‘quantile’
.layoutCreate: no visible global function definition for ‘layout’
.layoutCreate: no visible global function definition for ‘layout.show’
.notSubFrame: no visible global function definition for ‘chull’
.trackSlope : <anonymous>: no visible binding for global variable ‘C’
getPeaks: no visible global function definition for ‘sd’
getPeaks: no visible global function definition for ‘median’
plotDens: no visible global function definition for ‘densCols’
Undefined global functions or variables:
  C abline chull colors densCols density layout layout.show magnitude
  median mtext par polygon quantile remove.margins sd smooth.spline
  splinefun
Consider adding
  importFrom("grDevices", "chull", "colors", "densCols")
  importFrom("graphics", "abline", "layout", "layout.show", "mtext",
             "par", "polygon")
  importFrom("stats", "C", "density", "median", "quantile", "sd",
             "smooth.spline", "splinefun")
to your NAMESPACE file.
* 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 'GatingHierarchy,ANY,logical,ANY'
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 ... WARNING
Codoc mismatches from documentation object 'getPeaks':
getPeaks
  Code: function(frame, channel, tinypeak.removal = 1/25, verbose = F,
                 ...)
  Docs: function(frame, channel, tinypeak.removal = 1/25, ...)
  Argument names in code not in docs:
    verbose
  Mismatches in argument names:
    Position: 4 Code: verbose Docs: ...

* checking Rd \usage sections ... WARNING
Bad \usage lines found in documentation object 'flowDensity-methods':
  <unescaped bksl>S4method{flowDensity}{CellPopulation, ANY, logical, missing}(obj, channels, position, ...)
  <unescaped bksl>S4method{flowDensity}{flowFrame,ANY, logical, missing)}(obj, channels, position, ...)
  <unescaped bksl>S4method{flowDensity}{GatingHierarchy, ANY, logical, ANY}(obj, channels, position,node, ...)

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 ... 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: 4 WARNINGs, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-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	0.000	0.002
deGate	0.154	0.016	0.182
flowDensity	0.362	0.009	0.380
getPeaks	0.026	0.003	0.028
getflowFrame	0.558	0.012	0.578
nmRemove	0.215	0.013	0.233
notSubFrame	0.210	0.010	0.226
plotDens	0.126	0.010	0.144