BioC 2.14: CHECK report for RedeR on petty

Package: RedeR

Version: 1.12.9

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RedeR_1.12.9.tar.gz

StartedAt: 2014-10-07 23:45:35 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 23:47:04 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 89.1 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 --no-multiarch RedeR_1.12.9.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/RedeR.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘1.12.9’
* 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 ... [7s/7s] 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 ... 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 files in ‘vignettes’ ... OK
* 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 was 1 note.
See
  ‘/Users/biocbuild/bbs-2.14-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	0.952	0.050	1.004
addEdgeBetweenContainers	0.006	0.001	0.007
addEdges	0.002	0.000	0.003
addGraph	0.004	0.001	0.004
addLegend	0.004	0.001	0.004
addNodes	0.002	0.000	0.003
addSeries	0.003	0.000	0.003
addSubgraph	0.003	0.001	0.004
addSubgraph.list	0.003	0.000	0.003
att	0.112	0.013	0.126
calld	0.001	0.000	0.001
cea	0.076	0.011	0.087
deSelectEdges	0.003	0.000	0.003
deSelectGraph	0.002	0.000	0.003
deSelectNodes	0.003	0.001	0.003
deleteEdges	0.002	0.000	0.002
deleteNodes	0.003	0.000	0.003
deleteSelectedEdges	0.003	0.000	0.003
deleteSelectedNodes	0.003	0.000	0.003
duplicateGraph	0.003	0.000	0.003
exitd	0.002	0.000	0.002
getContainerComponets	0.004	0.001	0.005
getEdgeIDs	0.003	0.001	0.003
getEdges	0.003	0.001	0.003
getGraph	0.002	0.000	0.003
getNodeIDs	0.003	0.000	0.002
getNodes	0.002	0.000	0.003
getSourceEdgeIDs	0.002	0.000	0.002
getTargetEdgeIDs	0.003	0.001	0.003
gtoy.rm	0.001	0.000	0.002
isDynamicsActive	0.002	0.000	0.003
mergeNodes	0.003	0.001	0.003
mergeOutEdges	0.003	0.001	0.003
nestNodes	0.003	0.000	0.003
nesthc	0.002	0.000	0.003
ping	0.003	0.000	0.003
relax	0.005	0.001	0.005
resetd	0.002	0.001	0.002
selectAllEdges	0.003	0.001	0.004
selectAllNodes	0.003	0.001	0.003
selectEdges	0.003	0.000	0.003
selectGraph	0.003	0.000	0.003
selectNodes	0.002	0.000	0.003
setArrowDirection	0.002	0.000	0.003
subg	0.14	0.02	0.16
updateContainerSize	0.003	0.000	0.003
updateGraph	0.003	0.001	0.003
version	0.002	0.000	0.002