BioC 3.3: CHECK report for RedeR on oaxaca

Package: RedeR

Version: 1.20.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RedeR_1.20.0.tar.gz

StartedAt: 2016-10-13 05:35:30 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 05:36:16 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 46.8 seconds

RetCode: 0

Status:  OK

CheckDir: RedeR.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RedeR_1.20.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/RedeR.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RedeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RedeR’ 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 for sufficient/correct file permissions ... OK
* checking whether package ‘RedeR’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    java   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 ... NOTE
att.sete: no visible global function definition for ‘grey’
att.sete : colorcategory: no visible global function definition for
  ‘grey’
att.sete : colorcategory: no visible global function definition for
  ‘colorRampPalette’
att.sete : colorscale1: no visible global function definition for
  ‘quantile’
att.sete : colorscale1: no visible global function definition for
  ‘grey’
att.sete : colorscale1: no visible global function definition for
  ‘colorRampPalette’
att.sete : colorscale2: no visible global function definition for
  ‘quantile’
att.sete : colorscale2: no visible global function definition for
  ‘grey’
att.sete : colorscale2: no visible global function definition for
  ‘colorRampPalette’
att.sete : xscale: no visible global function definition for ‘quantile’
att.setv: no visible global function definition for ‘grey’
att.setv : colorcategory: no visible global function definition for
  ‘grey’
att.setv : colorcategory: no visible global function definition for
  ‘colorRampPalette’
att.setv : colorscale1: no visible global function definition for
  ‘quantile’
att.setv : colorscale1: no visible global function definition for
  ‘grey’
att.setv : colorscale1: no visible global function definition for
  ‘colorRampPalette’
att.setv : colorscale2: no visible global function definition for
  ‘quantile’
att.setv : colorscale2: no visible global function definition for
  ‘grey’
att.setv : colorscale2: no visible global function definition for
  ‘colorRampPalette’
att.setv : xscale: no visible global function definition for ‘quantile’
cea: no visible global function definition for ‘cor’
cea: no visible global function definition for ‘txtProgressBar’
cea: no visible global function definition for ‘density’
cea: no visible global function definition for ‘setTxtProgressBar’
cea: no visible global function definition for ‘p.adjust’
cea : ptcea: no visible global function definition for ‘density’
cea : ptcea: no visible global function definition for ‘hist’
cea : ptcea: no visible global function definition for ‘plot’
cea : ptcea: no visible global function definition for ‘polygon’
cea : ptcea: no visible global function definition for ‘lines’
cea : ptcea: no visible global function definition for ‘legend’
cea : ptcea: no visible global function definition for ‘rect’
gtoy.rm : nver: no visible global function definition for ‘runif’
gtoy.rm: no visible global function definition for ‘runif’
gtoy.rm: no visible global function definition for ‘terrain.colors’
addGraph,RedPort: no visible global function definition for
  ‘colorRampPalette’
addLegend.color,RedPort: no visible global function definition for
  ‘colorRampPalette’
addLegend.shape,RedPort: no visible global function definition for
  ‘colorRampPalette’
addLegend.size,RedPort: no visible global function definition for
  ‘colorRampPalette’
calld,RedPort : testInterface: no visible global function definition
  for ‘txtProgressBar’
calld,RedPort : testInterface: no visible global function definition
  for ‘setTxtProgressBar’
nestNodes,RedPort: no visible global function definition for
  ‘colorRampPalette’
nesthc,RedPort: no visible global function definition for
  ‘colorRampPalette’
nesthc,RedPort: no visible global function definition for ‘plot’
nesthc,RedPort: no visible global function definition for ‘par’
nesthc,RedPort: no visible global function definition for ‘text’
nesthc,RedPort: no visible global function definition for ‘rect’
Undefined global functions or variables:
  colorRampPalette cor density grey hist legend lines p.adjust par plot
  polygon quantile rect runif setTxtProgressBar terrain.colors text
  txtProgressBar
Consider adding
  importFrom("grDevices", "colorRampPalette", "grey", "terrain.colors")
  importFrom("graphics", "hist", "legend", "lines", "par", "plot",
             "polygon", "rect", "text")
  importFrom("stats", "cor", "density", "p.adjust", "quantile", "runif")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/RedeR.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
RedPort-class	0.003	0.001	0.003
RedPort	0.001	0.000	0.001
RedeR.data	0.566	0.028	0.595
addEdgeBetweenContainers	0.004	0.001	0.004
addEdges	0.001	0.000	0.001
addGraph	0.003	0.000	0.002
addLegend	0.002	0.000	0.002
addNodes	0.001	0.000	0.001
addSeries	0.001	0.000	0.002
addSubgraph	0.002	0.000	0.003
addSubgraph.list	0.001	0.000	0.002
att	0.087	0.007	0.093
calld	0.001	0.000	0.001
cea	0.059	0.005	0.063
deSelectEdges	0.001	0.000	0.001
deSelectGraph	0.002	0.000	0.002
deSelectNodes	0.002	0.000	0.002
deleteEdges	0.001	0.000	0.002
deleteNodes	0.001	0.000	0.002
deleteSelectedEdges	0.001	0.000	0.002
deleteSelectedNodes	0.001	0.000	0.001
duplicateGraph	0.001	0.000	0.001
exitd	0.002	0.000	0.002
getContainerComponets	0.002	0.000	0.003
getEdgeIDs	0.002	0.000	0.002
getEdges	0.001	0.000	0.002
getGraph	0.001	0.001	0.002
getNodeIDs	0.002	0.000	0.002
getNodes	0.001	0.000	0.002
getSourceEdgeIDs	0.001	0.001	0.002
getTargetEdgeIDs	0.002	0.000	0.002
gtoy.rm	0.001	0.000	0.001
isDynamicsActive	0.001	0.000	0.001
mergeNodes	0.001	0.000	0.001
mergeOutEdges	0.001	0.000	0.001
nestNodes	0.001	0.000	0.002
nesthc	0.001	0.000	0.001
ping	0.001	0.000	0.002
relax	0.002	0.001	0.002
resetd	0.001	0.000	0.001
selectAllEdges	0.001	0.000	0.001
selectAllNodes	0.002	0.001	0.002
selectEdges	0.001	0.000	0.002
selectGraph	0.001	0.000	0.002
selectNodes	0.001	0.000	0.001
setArrowDirection	0.002	0.000	0.001
subg	0.093	0.009	0.101
updateContainerSize	0.002	0.000	0.001
updateGraph	0.000	0.000	0.001
version	0.001	0.000	0.001