BioC 2.12: CHECK report for RedeR on petty

Package: RedeR

Version: 1.8.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RedeR_1.8.3.tar.gz

StartedAt: 2013-10-08 23:38:55 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 23:40:43 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 108.2 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 3.0.1 (2013-05-16)
* 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 '1.8.3'
* 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/10s] 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [8s/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
  '/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	0.026
PluginBuilder	0.024	0.001	0.025
RedPort-class	0.013	0.001	0.014
RedPort	0.010	0.001	0.011
RedeR.data	1.031	0.043	1.076
addEdgeBetweenContainers	0.023	0.001	0.023
addEdges	0.023	0.001	0.024
addGraph	0.030	0.001	0.031
addLegend	0.029	0.000	0.031
addNodes	0.025	0.001	0.025
addSeries	0.024	0.001	0.026
addSubgraph	0.115	0.006	0.121
addSubgraph.list	0.010	0.005	0.016
att	0.121	0.019	0.155
calld	0.006	0.003	0.009
cea	1.890	0.082	1.981
deSelectEdges	0.012	0.003	0.016
deSelectGraph	0.010	0.003	0.012
deSelectNodes	0.011	0.004	0.015
deleteEdges	0.010	0.002	0.012
deleteNodes	0.015	0.003	0.018
deletePlugin	0.014	0.003	0.018
deleteSelectedEdges	0.013	0.002	0.015
deleteSelectedNodes	0.014	0.003	0.018
duplicateGraph	0.011	0.003	0.014
dynwin	0.006	0.002	0.007
exitd	0.010	0.003	0.013
getArrowDirection	0.100	0.004	0.103
getContainerComponets	0.011	0.005	0.016
getEdgeColor	0.010	0.005	0.015
getEdgeIDs	0.006	0.003	0.010
getEdgeType	0.005	0.002	0.008
getEdgeWeight	0.008	0.003	0.011
getEdgeWidth	0.010	0.003	0.014
getEdges	0.009	0.003	0.012
getGraph	0.007	0.005	0.012
getNodeAliases	0.009	0.005	0.014
getNodeBend	0.009	0.004	0.013
getNodeColor	0.008	0.003	0.012
getNodeFontColor	0.010	0.003	0.013
getNodeFontName	0.008	0.003	0.014
getNodeFontSize	0.008	0.003	0.012
getNodeFontStyle	0.006	0.002	0.009
getNodeFontX	0.008	0.004	0.012
getNodeFontY	0.008	0.004	0.011
getNodeH	0.007	0.003	0.010
getNodeIDs	0.009	0.003	0.011
getNodeLineColor	0.011	0.003	0.014
getNodeLineWidth	0.010	0.004	0.013
getNodeShape	0.007	0.003	0.011
getNodeSize	0.009	0.004	0.014
getNodeW	0.010	0.004	0.014
getNodeWeight	0.009	0.003	0.012
getNodeX	0.008	0.003	0.011
getNodeY	0.010	0.003	0.014
getNodes	0.007	0.003	0.009
getSourceEdgeIDs	0.009	0.005	0.014
getSourceEdges	0.006	0.002	0.009
getTargetEdgeIDs	0.009	0.003	0.012
getTargetEdges	0.008	0.003	0.012
gtoy.rm	0.007	0.002	0.009
isDynamicsActive	0.008	0.001	0.010
mergeNodes	0.007	0.003	0.012
mergeOutEdges	0.010	0.005	0.017
nestNodes	0.011	0.004	0.019
nesthc	0.009	0.003	0.016
ping	0.009	0.003	0.013
pluginParser	0.005	0.002	0.124
relax	0.009	0.004	0.013
resetd	0.093	0.003	0.097
selectAllEdges	0.010	0.004	0.016
selectAllNodes	0.007	0.003	0.010
selectEdges	0.008	0.003	0.012
selectGraph	0.009	0.004	0.013
selectNodes	0.008	0.003	0.012
setArrowDirection	0.011	0.002	0.017
setEdgeColor	0.008	0.003	0.011
setEdgeType	0.009	0.005	0.013
setEdgeWeight	0.007	0.004	0.010
setEdgeWidth	0.009	0.003	0.012
setNodeAliases	0.008	0.003	0.012
setNodeBend	0.010	0.003	0.013
setNodeColor	0.008	0.002	0.011
setNodeFontColor	0.009	0.002	0.012
setNodeFontName	0.009	0.005	0.014
setNodeFontSize	0.006	0.004	0.010
setNodeFontStyle	0.007	0.003	0.010
setNodeFontXY	0.008	0.003	0.013
setNodeLineColor	0.010	0.004	0.016
setNodeLineWidth	0.010	0.004	0.014
setNodeShape	0.006	0.003	0.009
setNodeSize	0.009	0.003	0.011
setNodeWeight	0.009	0.004	0.014
setNodeXY	0.007	0.003	0.011
subg	0.143	0.015	0.158
submitPlugin	0.016	0.003	0.020
updateContainerSize	0.015	0.003	0.018
updateGraph	0.013	0.003	0.017
updatePlugins	0.007	0.003	0.011
version	0.011	0.003	0.014