BioC 2.13: CHECK report for RedeR on perceval

Package: RedeR

Version: 1.10.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RedeR_1.10.1.tar.gz

StartedAt: 2014-04-05 03:47:14 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 03:48:31 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 77.9 seconds

RetCode: 0

Status:  OK

CheckDir: RedeR.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/RedeR.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.10.1’
* 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 ... [6s/7s] OK
* checking installed package size ... NOTE
  installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    java   4.5Mb
* 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 ... NOTE
Namespace in Imports field not imported from: ‘rJava’
  All declared Imports should be used.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘RedeR.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [6s/7s] 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

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-2.13-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	0.008	0.001	0.011
PluginBuilder	0.018	0.001	0.019
RedPort-class	0.020	0.001	0.026
RedPort	0.007	0.000	0.007
RedeR.data	0.863	0.047	1.058
addEdgeBetweenContainers	0.012	0.006	0.019
addEdges	0.009	0.005	0.014
addGraph	0.021	0.008	0.031
addLegend	0.011	0.005	0.017
addNodes	0.007	0.004	0.011
addSeries	0.008	0.003	0.012
addSubgraph	0.013	0.005	0.019
addSubgraph.list	0.013	0.004	0.017
att	0.091	0.012	0.108
calld	0.009	0.003	0.023
cea	1.479	0.076	1.782
deSelectEdges	0.010	0.001	0.012
deSelectGraph	0.012	0.001	0.022
deSelectNodes	0.012	0.002	0.014
deleteEdges	0.012	0.001	0.014
deleteNodes	0.013	0.002	0.015
deletePlugin	0.006	0.001	0.008
deleteSelectedEdges	0.013	0.002	0.019
deleteSelectedNodes	0.013	0.001	0.015
duplicateGraph	0.013	0.001	0.014
dynwin	0.004	0.000	0.005
exitd	0.011	0.001	0.012
getContainerComponets	0.020	0.003	0.031
getEdgeIDs	0.021	0.003	0.024
getEdges	0.010	0.001	0.012
getGraph	0.008	0.001	0.010
getNodeIDs	0.012	0.002	0.014
getNodes	0.010	0.001	0.013
getSourceEdgeIDs	0.011	0.001	0.011
getTargetEdgeIDs	0.011	0.002	0.012
gtoy.rm	0.105	0.002	0.117
isDynamicsActive	0.005	0.003	0.009
mergeNodes	0.009	0.004	0.013
mergeOutEdges	0.011	0.005	0.021
nestNodes	0.010	0.006	0.016
nesthc	0.008	0.004	0.027
ping	0.010	0.004	0.024
pluginParser	0.004	0.002	0.007
relax	0.011	0.006	0.018
resetd	0.006	0.003	0.010
selectAllEdges	0.009	0.004	0.013
selectAllNodes	0.007	0.004	0.011
selectEdges	0.009	0.004	0.014
selectGraph	0.010	0.006	0.015
selectNodes	0.006	0.002	0.009
setArrowDirection	0.009	0.004	0.033
subg	0.090	0.015	0.106
submitPlugin	0.005	0.002	0.006
updateContainerSize	0.013	0.001	0.015
updateGraph	0.011	0.001	0.016
updatePlugins	0.010	0.002	0.012
version	0.015	0.002	0.017