BioC 2.12: CHECK report for RedeR on george2

Package: RedeR

Version: 1.8.3

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings RedeR_1.8.3.tar.gz

StartedAt: 2013-10-09 04:25:47 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 04:27:26 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 98.9 seconds

RetCode: 0

Status:  OK

CheckDir: RedeR.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/RedeR.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-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 ‘1.8.3’
* 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 ‘RedeR’ can be installed ... [9s/9s] OK
* checking installed package size ... NOTE
  installed size is  9.2Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    java   4.5Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENCE
is not mentioned in the DESCRIPTION file.
* 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 for unstated 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 ... OK
* 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 examples ... [9s/9s] 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-2.12-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
PluginBuilder-class	0.036	0.000	0.037
PluginBuilder	0.044	0.004	0.046
RedPort-class	0.008	0.000	0.008
RedPort	0.008	0.004	0.016
RedeR.data	1.008	0.016	1.024
addEdgeBetweenContainers	0.016	0.008	0.021
addEdges	0.012	0.000	0.013
addGraph	0.024	0.000	0.026
addLegend	0.024	0.000	0.023
addNodes	0.016	0.000	0.015
addSeries	0.016	0.000	0.019
addSubgraph	0.028	0.008	0.034
addSubgraph.list	0.020	0.000	0.019
att	0.104	0.004	0.107
calld	0.016	0.000	0.017
cea	1.804	0.036	1.839
deSelectEdges	0.028	0.000	0.030
deSelectGraph	0.028	0.000	0.028
deSelectNodes	0.020	0.000	0.021
deleteEdges	0.016	0.000	0.016
deleteNodes	0.024	0.000	0.024
deletePlugin	0.024	0.000	0.022
deleteSelectedEdges	0.020	0.004	0.025
deleteSelectedNodes	0.024	0.000	0.024
duplicateGraph	0.028	0.000	0.025
dynwin	0.024	0.000	0.024
exitd	0.024	0.000	0.024
getArrowDirection	0.024	0.000	0.026
getContainerComponets	0.016	0.008	0.026
getEdgeColor	0.008	0.008	0.016
getEdgeIDs	0.012	0.008	0.021
getEdgeType	0.016	0.008	0.023
getEdgeWeight	0.008	0.008	0.016
getEdgeWidth	0.024	0.020	0.046
getEdges	0.028	0.004	0.031
getGraph	0.016	0.008	0.022
getNodeAliases	0.020	0.012	0.032
getNodeBend	0.008	0.004	0.013
getNodeColor	0.008	0.008	0.017
getNodeFontColor	0.012	0.000	0.014
getNodeFontName	0.008	0.008	0.017
getNodeFontSize	0.008	0.008	0.018
getNodeFontStyle	0.004	0.012	0.012
getNodeFontX	0.012	0.008	0.019
getNodeFontY	0.000	0.012	0.015
getNodeH	0.012	0.004	0.016
getNodeIDs	0.016	0.004	0.018
getNodeLineColor	0.008	0.008	0.014
getNodeLineWidth	0.012	0.004	0.017
getNodeShape	0.012	0.008	0.020
getNodeSize	0.012	0.004	0.015
getNodeW	0.012	0.008	0.018
getNodeWeight	0.008	0.012	0.020
getNodeX	0.004	0.012	0.015
getNodeY	0.020	0.000	0.021
getNodes	0.008	0.008	0.016
getSourceEdgeIDs	0.016	0.000	0.028
getSourceEdges	0.016	0.004	0.020
getTargetEdgeIDs	0.012	0.004	0.013
getTargetEdges	0.012	0.004	0.018
gtoy.rm	0.004	0.004	0.010
isDynamicsActive	0.008	0.004	0.013
mergeNodes	0.016	0.004	0.020
mergeOutEdges	0.012	0.008	0.022
nestNodes	0.012	0.008	0.018
nesthc	0.008	0.008	0.014
ping	0.020	0.004	0.020
pluginParser	0.008	0.004	0.012
relax	0.016	0.012	0.057
resetd	0.004	0.012	0.016
selectAllEdges	0.020	0.004	0.026
selectAllNodes	0.012	0.004	0.015
selectEdges	0.012	0.008	0.017
selectGraph	0.016	0.004	0.021
selectNodes	0.012	0.004	0.015
setArrowDirection	0.012	0.008	0.018
setEdgeColor	0.184	0.012	0.195
setEdgeType	0.020	0.004	0.026
setEdgeWeight	0.012	0.008	0.019
setEdgeWidth	0.004	0.012	0.016
setNodeAliases	0.012	0.004	0.018
setNodeBend	0.016	0.008	0.022
setNodeColor	0.008	0.008	0.014
setNodeFontColor	0.012	0.004	0.018
setNodeFontName	0.016	0.000	0.016
setNodeFontSize	0.016	0.004	0.021
setNodeFontStyle	0.008	0.012	0.022
setNodeFontXY	0.020	0.000	0.018
setNodeLineColor	0.016	0.008	0.022
setNodeLineWidth	0.012	0.012	0.020
setNodeShape	0.024	0.008	0.031
setNodeSize	0.012	0.004	0.018
setNodeWeight	0.008	0.008	0.015
setNodeXY	0.008	0.008	0.020
subg	0.104	0.004	0.106
submitPlugin	0.032	0.000	0.033
updateContainerSize	0.020	0.000	0.022
updateGraph	0.028	0.000	0.029
updatePlugins	0.016	0.004	0.020
version	0.008	0.008	0.016