BioC 3.1: CHECK report for RedeR on petty

Package: RedeR

Version: 1.16.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RedeR_1.16.0.tar.gz

StartedAt: 2015-10-09 01:30:25 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 01:31:36 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 70.9 seconds

RetCode: 0

Status:  OK

CheckDir: RedeR.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RedeR_1.16.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/RedeR.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* 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 ‘1.16.0’
* 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 ... [5s/5s] OK
* checking installed package size ... NOTE
  installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    java   4.3Mb
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
addSubgraph,RedPort : .local: no visible global function definition for
  ‘G<-’
addSubgraph.list,RedPort : .local: no visible global function
  definition for ‘G<-’
nesthc,RedPort : .local: no visible global function definition for
  ‘pvpick’
* 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 files in ‘vignettes’ ... OK
* checking examples ... [3s/3s] 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
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-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
RedPort-class	0.003	0.000	0.004
RedPort	0.002	0.000	0.002
RedeR.data	0.757	0.048	0.806
addEdgeBetweenContainers	0.008	0.001	0.007
addEdges	0.003	0.000	0.003
addGraph	0.005	0.000	0.005
addLegend	0.004	0.001	0.003
addNodes	0.003	0.000	0.002
addSeries	0.002	0.000	0.002
addSubgraph	0.002	0.001	0.002
addSubgraph.list	0.002	0.000	0.002
att	0.137	0.011	0.147
calld	0.002	0.001	0.002
cea	0.083	0.008	0.091
deSelectEdges	0.002	0.001	0.002
deSelectGraph	0.003	0.000	0.003
deSelectNodes	0.002	0.000	0.003
deleteEdges	0.001	0.000	0.002
deleteNodes	0.002	0.000	0.002
deleteSelectedEdges	0.002	0.000	0.001
deleteSelectedNodes	0.001	0.001	0.001
duplicateGraph	0.002	0.000	0.003
exitd	0.002	0.001	0.002
getContainerComponets	0.005	0.000	0.004
getEdgeIDs	0.002	0.000	0.003
getEdges	0.003	0.000	0.003
getGraph	0.002	0.000	0.002
getNodeIDs	0.002	0.000	0.003
getNodes	0.003	0.000	0.003
getSourceEdgeIDs	0.002	0.001	0.003
getTargetEdgeIDs	0.001	0.000	0.002
gtoy.rm	0.000	0.000	0.001
isDynamicsActive	0.003	0.000	0.002
mergeNodes	0.002	0.000	0.003
mergeOutEdges	0.003	0.000	0.002
nestNodes	0.002	0.001	0.003
nesthc	0.001	0.000	0.001
ping	0.001	0.000	0.002
relax	0.003	0.000	0.004
resetd	0.002	0.000	0.003
selectAllEdges	0.003	0.001	0.003
selectAllNodes	0.003	0.000	0.003
selectEdges	0.002	0.001	0.003
selectGraph	0.002	0.000	0.003
selectNodes	0.003	0.000	0.002
setArrowDirection	0.002	0.000	0.002
subg	0.136	0.016	0.152
updateContainerSize	0.002	0.000	0.002
updateGraph	0.003	0.000	0.002
version	0.002	0.000	0.003