Package: RedeR

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RedeR_1.8.0.tar.gz

StartedAt: 2013-05-01 10:02:02 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 10:03:39 -0700 (Wed, 01 May 2013)

EllapsedTime: 96.9 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 Patched (2013-04-08 r62531)
* 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 '1.8.0'
* 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 ... [8s/9s] OK
* checking installed package size ... NOTE
  installed size is  9.1Mb
  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 ... NOTE
File 'RedeR/R/zzz.R':
  .onLoad calls:
    packageStartupMessage(msg, appendLF = FALSE)

See section 'Good practice' in '?.onAttach'.
* 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 3 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
** testing if installed package can be loaded
* DONE (RedeR)

name	user	system	elapsed
PluginBuilder-class	0.026	0.001	0.027
PluginBuilder	0.032	0.002	0.034
RedPort-class	0.017	0.001	0.017
RedPort	0.010	0.001	0.011
RedeR.data	1.035	0.061	1.108
addEdgeBetweenContainers	0.013	0.007	0.021
addEdges	0.009	0.006	0.015
addGraph	0.019	0.011	0.030
addLegend	0.015	0.008	0.024
addNodes	0.006	0.004	0.010
addSeries	0.011	0.004	0.016
addSubgraph	0.018	0.005	0.023
addSubgraph.list	0.011	0.005	0.017
att	0.104	0.016	0.129
calld	0.010	0.003	0.012
cea	1.707	0.083	1.810
deSelectEdges	0.015	0.003	0.019
deSelectGraph	0.013	0.003	0.016
deSelectNodes	0.015	0.003	0.019
deleteEdges	0.013	0.004	0.017
deleteNodes	0.011	0.004	0.016
deletePlugin	0.012	0.004	0.017
deleteSelectedEdges	0.020	0.005	0.025
deleteSelectedNodes	0.010	0.003	0.014
duplicateGraph	0.010	0.004	0.014
dynwin	0.008	0.003	0.011
exitd	0.011	0.005	0.016
getArrowDirection	0.013	0.005	0.019
getContainerComponets	0.014	0.005	0.019
getEdgeColor	0.098	0.007	0.106
getEdgeIDs	0.009	0.005	0.021
getEdgeType	0.009	0.006	0.018
getEdgeWeight	0.009	0.006	0.016
getEdgeWidth	0.010	0.005	0.015
getEdges	0.009	0.005	0.016
getGraph	0.006	0.004	0.011
getNodeAliases	0.008	0.005	0.014
getNodeBend	0.006	0.005	0.011
getNodeColor	0.009	0.004	0.013
getNodeFontColor	0.010	0.006	0.015
getNodeFontName	0.007	0.004	0.011
getNodeFontSize	0.008	0.005	0.013
getNodeFontStyle	0.007	0.005	0.012
getNodeFontX	0.009	0.004	0.015
getNodeFontY	0.010	0.006	0.015
getNodeH	0.007	0.004	0.011
getNodeIDs	0.010	0.005	0.014
getNodeLineColor	0.010	0.006	0.017
getNodeLineWidth	0.006	0.004	0.011
getNodeShape	0.009	0.005	0.014
getNodeSize	0.008	0.006	0.014
getNodeW	0.010	0.005	0.014
getNodeWeight	0.011	0.006	0.020
getNodeX	0.007	0.004	0.013
getNodeY	0.010	0.005	0.015
getNodes	0.012	0.007	0.019
getSourceEdgeIDs	0.009	0.004	0.013
getSourceEdges	0.011	0.005	0.016
getTargetEdgeIDs	0.009	0.006	0.015
getTargetEdges	0.011	0.005	0.016
gtoy.rm	0.006	0.003	0.009
isDynamicsActive	0.007	0.005	0.012
mergeNodes	0.009	0.004	0.013
mergeOutEdges	0.011	0.006	0.016
nestNodes	0.009	0.007	0.016
nesthc	0.007	0.005	0.012
ping	0.010	0.005	0.015
pluginParser	0.005	0.003	0.009
relax	0.012	0.005	0.017
resetd	0.007	0.005	0.012
selectAllEdges	0.011	0.004	0.019
selectAllNodes	0.009	0.005	0.019
selectEdges	0.007	0.005	0.012
selectGraph	0.009	0.004	0.015
selectNodes	0.007	0.005	0.013
setArrowDirection	0.010	0.004	0.022
setEdgeColor	0.009	0.006	0.015
setEdgeType	0.007	0.004	0.012
setEdgeWeight	0.009	0.005	0.015
setEdgeWidth	0.010	0.007	0.017
setNodeAliases	0.008	0.003	0.012
setNodeBend	0.011	0.006	0.019
setNodeColor	0.007	0.004	0.013
setNodeFontColor	0.009	0.004	0.015
setNodeFontName	0.010	0.006	0.023
setNodeFontSize	0.008	0.004	0.013
setNodeFontStyle	0.009	0.005	0.014
setNodeFontXY	0.006	0.004	0.012
setNodeLineColor	0.010	0.004	0.013
setNodeLineWidth	0.009	0.006	0.015
setNodeShape	0.007	0.004	0.012
setNodeSize	0.009	0.005	0.015
setNodeWeight	0.010	0.007	0.017
setNodeXY	0.006	0.004	0.011
subg	0.121	0.017	0.139
submitPlugin	0.015	0.004	0.020
updateContainerSize	0.013	0.002	0.016
updateGraph	0.013	0.002	0.015
updatePlugins	0.009	0.001	0.012
version	0.012	0.004	0.016