Package: RedeR

Version: 1.3.1

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RedeR_1.3.1.tar.gz

StartedAt: 2012-06-21 03:03:55 -0700 (Thu, 21 Jun 2012)

EndedAt: 2012-06-21 03:05:38 -0700 (Thu, 21 Jun 2012)

EllapsedTime: 103.0 seconds

RetCode: 0

Status:  OK

CheckDir: RedeR.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/RedeR.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'RedeR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RedeR' version '1.3.1'
* 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 whether package 'RedeR' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    1.3Mb
    java   4.5Mb
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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' ... NOTE
The following files should probably not be installed:
  'fig1.pdf', 'fig2.pdf', 'fig3.pdf', 'fig4.pdf', 'fig5a.pdf',
  'fig5b.pdf', 'fig5c.pdf', 'fig6.pdf'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking examples ... 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-2.11-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
   'RedeR.Rnw' 
** testing if installed package can be loaded

* DONE (RedeR)

name	user	system	elapsed
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PluginBuilder	0.002	0.001	0.003
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RedPort	0.001	0.000	0.001
RedeR.data	0.881	0.044	0.937
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addSubgraph	0.001	0.000	0.001
addSubgraph.list	0.000	0.000	0.001
att	0.119	0.007	0.127
calld	0.001	0.001	0.001
cea	1.933	0.284	2.277
deSelectEdges	0.001	0.000	0.001
deSelectGraph	0.001	0.000	0.001
deSelectNodes	0.001	0.000	0.001
deleteEdges	0.001	0.001	0.001
deleteNodes	0.001	0.000	0.001
deletePlugin	0.001	0.000	0.001
deleteSelectedEdges	0.000	0.000	0.001
deleteSelectedNodes	0.001	0.000	0.001
duplicateGraph	0.001	0.000	0.001
dynwin	0	0	0
exitd	0.001	0.000	0.001
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getTargetEdges	0.001	0.000	0.001
gtoy.rm	3.086	0.078	3.234
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mergeNodes	0.001	0.001	0.001
mergeOutEdges	0.002	0.000	0.002
nestNodes	0.001	0.000	0.002
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ping	0.001	0.000	0.001
pluginParser	0.000	0.000	0.001
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selectEdges	0.001	0.000	0.001
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subg	0.293	0.020	0.319
submitPlugin	0.002	0.000	0.002
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updateGraph	0.001	0.000	0.001
updatePlugins	0.001	0.000	0.001
version	0.001	0.000	0.001