BioC 3.5: CHECK report for flowPloidy on oaxaca

Package: flowPloidy

Version: 1.1.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings flowPloidy_1.1.3.tar.gz

StartedAt: 2017-03-04 02:54:41 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 02:56:41 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 119.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: flowPloidy.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 flowPloidy_1.1.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/flowPloidy.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowPloidy/DESCRIPTION’ ... OK
* this is package ‘flowPloidy’ version ‘1.1.3’
* 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 ‘flowPloidy’ can be installed ... OK
* 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
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
browseFlowHist : server: no visible global function definition for
  ‘reactiveValues’
browseFlowHist : server: no visible global function definition for
  ‘observeEvent’
browseFlowHist : server: no visible global function definition for
  ‘updateNumericInput’
browseFlowHist : server: no visible binding for global variable
  ‘prefix’
browseFlowHist : server: no visible global function definition for
  ‘brushedPoints’
browseFlowHist : server: no visible global function definition for
  ‘updateSliderInput’
gateFlowHist : server: no visible global function definition for
  ‘updateSliderInput’
gateFlowHist : server: no visible global function definition for
  ‘brushedPoints’
Undefined global functions or variables:
  brushedPoints observeEvent prefix reactiveValues updateNumericInput
  updateSliderInput
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'FlowHist.Rd':
  ‘caTools::runmax’ ‘caTools::runmean’ ‘histBatch’ ‘modelComponent’

Missing link or links in documentation object 'findPeaks.Rd':
  ‘caTools::runmax’ ‘caTools::runmean’

Missing link or links in documentation object 'pickInit.Rd':
  ‘pickPeaks’

See section 'Cross-references' in the 'Writing R Extensions' manual.

* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'plot.FlowHist'
  ‘main’

Undocumented arguments in documentation object 'plotFH'
  ‘main’

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 ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
FlowHist 5.403  0.164   6.214
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/flowPloidy.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
FlowHist	5.403	0.164	6.214
browseFlowHist	2.938	0.077	3.016
fhAnalyze	0.267	0.008	0.275
findPeaks	0.001	0.000	0.001
pickInit	0.421	0.005	0.426
plotFH	0.194	0.004	0.213
setBins	0.300	0.011	0.312
tabulateFlowHist	0.319	0.013	0.332
updateFlowHist	0.334	0.013	0.348
viewFlowChannels	0.030	0.001	0.032