Package: KEGGgraph

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/2.12/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch KEGGgraph_1.6.0.tar.gz

StartedAt: 2011-03-31 06:25:35 -0700 (Thu, 31 Mar 2011)

EndedAt: 2011-03-31 06:27:49 -0700 (Thu, 31 Mar 2011)

EllapsedTime: 134.0 seconds

RetCode: 0

Status:  OK

CheckDir: KEGGgraph.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.7-bioc/meat/KEGGgraph.Rcheck’
* using R version 2.12.2 Patched (2011-02-25 r54591)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘KEGGgraph/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘KEGGgraph’ version ‘1.6.0’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘KEGGgraph’ can be installed ... OK
* 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 ... NOTE
.subtypeDisplay: no visible binding for global variable
  ‘KEGGEdgeSubtype’
KEGGgraphLegend: no visible binding for global variable
  ‘KEGGEdgeSubtype’
* 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 data for non-ASCII characters ... OK
* checking examples ... OK
* checking for unstated dependencies in tests ... NOTE
'library' or 'require' call not declared from: RUnit
* checking tests ...
  Running ‘kegg2graph.R’
  Running ‘testGraph.R’
 OK
* checking package vignettes in ‘inst/doc’ ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package ‘KEGGgraph’ ...
** R
** data
** inst
** preparing package for lazy loading

Attaching package: 'graph'

The following object(s) are masked from 'package:XML':

    addNode

Loading required package: grid
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (KEGGgraph)

name	user	system	elapsed
KEGGEdge-class	1.572	0.015	1.604
KEGGEdgeSubType-class	0.002	0.001	0.001
KEGGEdgeSubtype	0.014	0.002	0.016
KEGGGraphics-class	0.001	0.000	0.001
KEGGGroup-class	0.002	0.000	0.002
KEGGNode-class	0.843	0.004	0.850
KEGGPathway-class	1.443	0.014	1.468
KEGGPathwayInfo-class	0.889	0.006	0.910
KEGGReaction-class	1.516	0.009	1.547
KEGGpathway2Graph	0.993	0.010	1.015
KEGGpathway2reactionGraph	1.482	0.010	1.506
expandKEGGPathway	2.076	0.009	2.111
getDisplayName-methods	0.940	0.006	0.956
getEntryID-methods	0.832	0.005	0.843
getKEGGID-methods	0.436	0.003	0.442
getKEGGgeneLink-methods	0.000	0.000	0.001
getKEGGnodeData	2.469	0.014	2.514
getKGMLurl	0.008	0.018	0.027
getName-methods	0.853	0.021	0.884
getNamedElement	0.000	0.001	0.000
getPathwayInfo-methods	0.881	0.006	0.899
getReactions-methods	1.537	0.011	1.578
getRgraphvizEdgeNames	0.004	0.001	0.004
getSubtype-methods	0.921	0.005	0.939
getTitle-methods	0.975	0.012	0.999
getType-methods	1.389	0.009	1.425
graphDensity	0.005	0.001	0.005
isHomoList	0.002	0.000	0.001
mergeKEGGgraphs	4.547	0.024	4.625
neighborhood	0.035	0.001	0.035
parseKGML	0.899	0.005	0.925
parseKGML2Graph	2.334	0.011	2.374
plotKEGGgraph	5.024	0.033	5.123
pvalue2asterisk	0.000	0.000	0.001
queryKEGGsubgraph	2.528	0.010	2.554
randomSubGraph	0.048	0.000	0.049
splitKEGGgroup	0.866	0.005	0.871
subGraphByNodeType	2.444	0.007	2.454
subKEGGgraph	2.579	0.010	2.600
translateKEGGID2GeneID	0.001	0.001	0.001
translateKEGGgraph	2.428	0.006	2.439