BioC 2.13: CHECK report for RedeR on zin1

Package: RedeR

Version: 1.10.1

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings RedeR_1.10.1.tar.gz

StartedAt: 2014-04-05 03:27:04 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 03:27:47 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 42.9 seconds

RetCode: 0

Status:  OK

CheckDir: RedeR.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/RedeR.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.10.1’
* 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 ... [3s/3s] OK
* checking installed package size ... NOTE
  installed size is  9.0Mb
  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 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 ... [4s/4s] 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
  ‘/home/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	0.004	0.000	0.005
PluginBuilder	0.008	0.000	0.007
RedPort-class	0.008	0.000	0.005
RedPort	0.004	0.000	0.004
RedeR.data	0.612	0.016	0.650
addEdgeBetweenContainers	0.004	0.004	0.007
addEdges	0.000	0.004	0.004
addGraph	0.008	0.000	0.007
addLegend	0.004	0.004	0.009
addNodes	0.004	0.000	0.004
addSeries	0.004	0.000	0.005
addSubgraph	0.004	0.000	0.005
addSubgraph.list	0.004	0.000	0.004
att	0.076	0.000	0.077
calld	0.004	0.000	0.003
cea	1.128	0.012	1.156
deSelectEdges	0.004	0.000	0.004
deSelectGraph	0.004	0.000	0.004
deSelectNodes	0.004	0.000	0.004
deleteEdges	0.004	0.000	0.004
deleteNodes	0.008	0.000	0.004
deletePlugin	0.004	0.000	0.002
deleteSelectedEdges	0.008	0.000	0.005
deleteSelectedNodes	0.004	0.000	0.004
duplicateGraph	0.004	0.000	0.004
dynwin	0.000	0.000	0.001
exitd	0.004	0.000	0.004
getContainerComponets	0.004	0.000	0.004
getEdgeIDs	0.004	0.000	0.003
getEdges	0.000	0.000	0.003
getGraph	0.004	0.000	0.003
getNodeIDs	0.004	0.000	0.004
getNodes	0.004	0.000	0.003
getSourceEdgeIDs	0.004	0.000	0.004
getTargetEdgeIDs	0.004	0.000	0.004
gtoy.rm	0.052	0.000	0.051
isDynamicsActive	0.000	0.004	0.004
mergeNodes	0.004	0.000	0.005
mergeOutEdges	0.008	0.000	0.007
nestNodes	0.000	0.004	0.004
nesthc	0.000	0.000	0.003
ping	0.004	0.000	0.004
pluginParser	0.000	0.000	0.002
relax	0.004	0.004	0.011
resetd	0.000	0.004	0.003
selectAllEdges	0.008	0.000	0.004
selectAllNodes	0.000	0.004	0.003
selectEdges	0.004	0.000	0.004
selectGraph	0.004	0.000	0.005
selectNodes	0.000	0.004	0.004
setArrowDirection	0.000	0.004	0.005
subg	0.072	0.008	0.084
submitPlugin	0.000	0.000	0.002
updateContainerSize	0.004	0.000	0.004
updateGraph	0.000	0.000	0.003
updatePlugins	0.004	0.000	0.002
version	0.004	0.000	0.004