Package: KEGGgraph

Version: 1.7.0

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch KEGGgraph_1.7.0.tar.gz

StartedAt: 2011-02-24 16:02:42 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 16:04:17 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 95.2 seconds

RetCode: 0

Status:  OK

CheckDir: KEGGgraph.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/KEGGgraph.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'KEGGgraph/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'KEGGgraph' version '1.7.0'
* 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	1.183	0.006	1.189
KEGGEdgeSubType-class	0	0	0
KEGGEdgeSubtype	0.009	0.001	0.010
KEGGGraphics-class	0.001	0.000	0.000
KEGGGroup-class	0.001	0.000	0.001
KEGGNode-class	0.666	0.002	0.668
KEGGPathway-class	1.110	0.005	1.115
KEGGPathwayInfo-class	0.625	0.002	0.627
KEGGReaction-class	1.097	0.003	1.100
KEGGpathway2Graph	0.792	0.003	0.795
KEGGpathway2reactionGraph	1.116	0.002	1.120
expandKEGGPathway	1.531	0.002	1.533
getDisplayName-methods	0.644	0.003	0.647
getEntryID-methods	0.699	0.004	0.702
getKEGGID-methods	0.328	0.001	0.330
getKEGGgeneLink-methods	0.001	0.000	0.000
getKEGGnodeData	1.772	0.004	1.776
getKGMLurl	0.005	0.003	0.009
getName-methods	0.676	0.002	0.678
getNamedElement	0.001	0.001	0.000
getPathwayInfo-methods	0.674	0.003	0.676
getReactions-methods	1.090	0.003	1.093
getRgraphvizEdgeNames	0.002	0.001	0.003
getSubtype-methods	0.602	0.001	0.603
getTitle-methods	0.614	0.002	0.616
getType-methods	1.070	0.002	1.072
graphDensity	0.003	0.000	0.004
isHomoList	0.001	0.000	0.000
mergeKEGGgraphs	3.399	0.005	3.404
neighborhood	0.025	0.000	0.025
parseKGML	0.688	0.004	0.692
parseKGML2Graph	1.705	0.002	1.708
plotKEGGgraph	3.707	0.009	3.716
pvalue2asterisk	0.001	0.000	0.000
queryKEGGsubgraph	1.771	0.010	1.780
randomSubGraph	0.031	0.000	0.032
splitKEGGgroup	0.669	0.001	0.671
subGraphByNodeType	1.849	0.002	1.850
subKEGGgraph	1.959	0.003	1.961
translateKEGGID2GeneID	0.000	0.000	0.001
translateKEGGgraph	1.773	0.002	1.775