Package: RedeR

Version: 1.6.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RedeR_1.6.2.tar.gz

StartedAt: 2013-03-24 09:25:38 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 09:27:15 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 97.0 seconds

RetCode: 0

Status:  OK

CheckDir: RedeR.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/RedeR.Rcheck'
* using R version 3.0.0 beta (2013-03-21 r62346)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'RedeR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RedeR' version '1.6.2'
* 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 ... [8s/8s] 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
  '/Users/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
   'RedeR.Rnw' 
** testing if installed package can be loaded
* DONE (RedeR)

name	user	system	elapsed
PluginBuilder-class	0.020	0.001	0.022
PluginBuilder	0.026	0.001	0.027
RedPort-class	0.013	0.001	0.013
RedPort	0.012	0.001	0.013
RedeR.data	1.018	0.052	1.109
addEdgeBetweenContainers	0.012	0.007	0.019
addEdges	0.008	0.005	0.014
addGraph	0.017	0.010	0.026
addLegend	0.017	0.008	0.024
addNodes	0.009	0.003	0.011
addSeries	0.011	0.003	0.014
addSubgraph	0.017	0.010	0.027
addSubgraph.list	0.013	0.006	0.018
att	0.121	0.016	0.143
calld	0.009	0.002	0.010
cea	1.705	0.067	1.773
deSelectEdges	0.012	0.003	0.015
deSelectGraph	0.013	0.003	0.017
deSelectNodes	0.013	0.003	0.017
deleteEdges	0.014	0.004	0.017
deleteNodes	0.014	0.003	0.016
deletePlugin	0.014	0.003	0.018
deleteSelectedEdges	0.013	0.004	0.017
deleteSelectedNodes	0.013	0.003	0.017
duplicateGraph	0.016	0.004	0.020
dynwin	0.009	0.002	0.011
exitd	0.007	0.006	0.013
getArrowDirection	0.010	0.005	0.015
getContainerComponets	0.012	0.006	0.018
getEdgeColor	0.010	0.006	0.015
getEdgeIDs	0.007	0.005	0.012
getEdgeType	0.011	0.006	0.016
getEdgeWeight	0.011	0.006	0.022
getEdgeWidth	0.011	0.007	0.019
getEdges	0.008	0.007	0.015
getGraph	0.011	0.005	0.018
getNodeAliases	0.012	0.007	0.020
getNodeBend	0.009	0.004	0.013
getNodeColor	0.013	0.006	0.020
getNodeFontColor	0.010	0.007	0.016
getNodeFontName	0.007	0.004	0.011
getNodeFontSize	0.009	0.004	0.015
getNodeFontStyle	0.008	0.005	0.014
getNodeFontX	0.007	0.004	0.011
getNodeFontY	0.010	0.005	0.014
getNodeH	0.009	0.006	0.015
getNodeIDs	0.008	0.005	0.012
getNodeLineColor	0.010	0.005	0.016
getNodeLineWidth	0.010	0.006	0.016
getNodeShape	0.008	0.005	0.012
getNodeSize	0.010	0.004	0.015
getNodeW	0.009	0.005	0.014
getNodeWeight	0.010	0.006	0.016
getNodeX	0.007	0.004	0.012
getNodeY	0.009	0.004	0.013
getNodes	0.009	0.006	0.015
getSourceEdgeIDs	0.007	0.005	0.012
getSourceEdges	0.010	0.005	0.014
getTargetEdgeIDs	0.010	0.006	0.016
getTargetEdges	0.007	0.005	0.011
gtoy.rm	0.005	0.003	0.008
isDynamicsActive	0.009	0.004	0.013
mergeNodes	0.012	0.007	0.019
mergeOutEdges	0.007	0.005	0.013
nestNodes	0.010	0.005	0.015
nesthc	0.009	0.006	0.015
ping	0.012	0.006	0.019
pluginParser	0.006	0.004	0.010
relax	0.013	0.007	0.020
resetd	0.006	0.005	0.011
selectAllEdges	0.009	0.004	0.013
selectAllNodes	0.009	0.006	0.015
selectEdges	0.008	0.005	0.014
selectGraph	0.106	0.005	0.111
selectNodes	0.010	0.005	0.015
setArrowDirection	0.007	0.005	0.012
setEdgeColor	0.010	0.004	0.015
setEdgeType	0.011	0.006	0.016
setEdgeWeight	0.009	0.007	0.016
setEdgeWidth	0.010	0.005	0.016
setNodeAliases	0.009	0.006	0.015
setNodeBend	0.010	0.007	0.017
setNodeColor	0.009	0.005	0.015
setNodeFontColor	0.009	0.006	0.015
setNodeFontName	0.010	0.006	0.016
setNodeFontSize	0.007	0.005	0.012
setNodeFontStyle	0.010	0.005	0.016
setNodeFontXY	0.010	0.006	0.017
setNodeLineColor	0.008	0.005	0.012
setNodeLineWidth	0.010	0.006	0.015
setNodeShape	0.009	0.006	0.016
setNodeSize	0.007	0.004	0.012
setNodeWeight	0.010	0.006	0.016
setNodeXY	0.010	0.006	0.016
subg	0.120	0.026	0.148
submitPlugin	0.016	0.004	0.021
updateContainerSize	0.012	0.005	0.020
updateGraph	0.008	0.005	0.014
updatePlugins	0.011	0.004	0.015
version	0.008	0.004	0.012