BioC 3.5: CHECK report for RedeR on oaxaca

Package: RedeR

Version: 1.23.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RedeR_1.23.1.tar.gz

StartedAt: 2017-03-04 07:55:05 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 07:55:52 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 46.6 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_1.23.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/RedeR.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 ‘RedeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RedeR’ version ‘1.23.1’
* 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-3.5-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	0.001	0.000	0.002
RedPort	0.001	0.000	0.001
RedeR.data	0.486	0.018	0.504
addEdgeBetweenContainers	0.002	0.000	0.002
addEdges	0.001	0.000	0.001
addGraph	0.001	0.000	0.002
addLegend	0.001	0.000	0.001
addNodes	0.000	0.001	0.001
addSeries	0.001	0.000	0.001
addSubgraph	0.001	0.000	0.001
addSubgraph.list	0.001	0.000	0.001
att	0.379	0.009	0.387
calld	0.000	0.000	0.001
cea	0.041	0.003	0.044
deSelectEdges	0.001	0.000	0.001
deSelectGraph	0.001	0.000	0.001
deSelectNodes	0.001	0.000	0.001
deleteEdges	0.001	0.001	0.001
deleteNodes	0.001	0.000	0.001
deleteSelectedEdges	0.001	0.000	0.001
deleteSelectedNodes	0.001	0.000	0.001
duplicateGraph	0.001	0.000	0.001
exitd	0.000	0.001	0.000
getContainerComponets	0.004	0.000	0.005
getEdgeIDs	0.001	0.000	0.001
getEdges	0	0	0
getGraph	0.001	0.001	0.001
getNodeIDs	0.000	0.000	0.001
getNodes	0.001	0.000	0.000
getSourceEdgeIDs	0.000	0.000	0.001
getTargetEdgeIDs	0.001	0.000	0.001
gtoy.rm	0	0	0
isDynamicsActive	0.000	0.001	0.001
mergeNodes	0.001	0.000	0.001
mergeOutEdges	0.000	0.000	0.001
nestNodes	0.001	0.000	0.001
nesthc	0	0	0
ping	0.001	0.000	0.001
relax	0.002	0.000	0.001
resetd	0.000	0.000	0.001
selectAllEdges	0.001	0.000	0.001
selectAllNodes	0	0	0
selectEdges	0.001	0.001	0.001
selectGraph	0.001	0.000	0.001
selectNodes	0.001	0.000	0.001
setArrowDirection	0.001	0.000	0.001
subg	0.069	0.005	0.073
updateContainerSize	0.001	0.000	0.001
updateGraph	0.001	0.000	0.001
version	0.001	0.000	0.000