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BioC 3.4: CHECK report for RedeR on malbec1

This page was generated on 2017-04-15 16:10:31 -0400 (Sat, 15 Apr 2017).

Package 1028/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RedeR 1.22.0
Mauro Castro
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/RedeR
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RedeR
Version: 1.22.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings RedeR_1.22.0.tar.gz
StartedAt: 2017-04-15 00:49:01 -0400 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 00:49:39 -0400 (Sat, 15 Apr 2017)
EllapsedTime: 38.1 seconds
RetCode: 0
Status:  OK 
CheckDir: RedeR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings RedeR_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/RedeR.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (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 ‘1.22.0’
* 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 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
  ‘/home/biocbuild/bbs-3.4-bioc/meat/RedeR.Rcheck/00check.log’
for details.


RedeR.Rcheck/00install.out:

* 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)

RedeR.Rcheck/RedeR-Ex.timings:

nameusersystemelapsed
RedPort-class0.0040.0000.001
RedPort0.0000.0000.001
RedeR.data0.5200.0000.517
addEdgeBetweenContainers0.0040.0000.002
addEdges0.0000.0000.001
addGraph0.0040.0000.002
addLegend0.0000.0000.002
addNodes0.0000.0000.001
addSeries0.0000.0000.001
addSubgraph0.0000.0000.001
addSubgraph.list0.0000.0000.001
att0.0720.0000.070
calld000
cea0.0480.0040.050
deSelectEdges0.0000.0000.001
deSelectGraph0.0040.0000.001
deSelectNodes0.0000.0000.001
deleteEdges0.0000.0000.001
deleteNodes0.0000.0000.001
deleteSelectedEdges0.0000.0000.001
deleteSelectedNodes0.0040.0000.001
duplicateGraph000
exitd0.0000.0000.001
getContainerComponets0.0000.0000.002
getEdgeIDs0.0000.0000.001
getEdges0.0000.0040.001
getGraph0.0000.0000.001
getNodeIDs000
getNodes0.0000.0000.001
getSourceEdgeIDs0.0000.0000.001
getTargetEdgeIDs0.0000.0040.001
gtoy.rm0.0000.0000.001
isDynamicsActive0.0000.0000.001
mergeNodes0.0040.0000.001
mergeOutEdges0.0000.0000.002
nestNodes0.0000.0000.001
nesthc000
ping0.0000.0000.001
relax0.0040.0000.002
resetd000
selectAllEdges0.0000.0000.001
selectAllNodes0.0040.0000.001
selectEdges0.0000.0000.001
selectGraph0.0000.0000.001
selectNodes0.0000.0000.001
setArrowDirection0.0000.0000.001
subg0.0840.0000.081
updateContainerSize0.0000.0000.001
updateGraph0.0040.0000.001
version000