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: 2011-03-17 16:41:31 -0700 (Thu, 17 Mar 2011)

EndedAt: 2011-03-17 16:43:07 -0700 (Thu, 17 Mar 2011)

EllapsedTime: 96.0 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) (2011-03-06 r54683)
* 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 installed package size ... 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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	1.123	0.005	1.129
KEGGEdgeSubType-class	0.001	0.001	0.001
KEGGEdgeSubtype	0.008	0.001	0.010
KEGGGraphics-class	0.000	0.000	0.001
KEGGGroup-class	0.001	0.000	0.001
KEGGNode-class	0.636	0.002	0.639
KEGGPathway-class	1.060	0.003	1.063
KEGGPathwayInfo-class	0.640	0.002	0.642
KEGGReaction-class	1.082	0.003	1.084
KEGGpathway2Graph	0.781	0.002	0.782
KEGGpathway2reactionGraph	1.052	0.002	1.054
expandKEGGPathway	1.523	0.002	1.524
getDisplayName-methods	0.667	0.004	0.671
getEntryID-methods	0.642	0.003	0.645
getKEGGID-methods	0.313	0.001	0.315
getKEGGgeneLink-methods	0	0	0
getKEGGnodeData	1.720	0.006	1.726
getKGMLurl	0.004	0.002	0.008
getName-methods	0.665	0.001	0.666
getNamedElement	0	0	0
getPathwayInfo-methods	0.691	0.004	0.695
getReactions-methods	1.078	0.002	1.081
getRgraphvizEdgeNames	0.003	0.000	0.003
getSubtype-methods	0.621	0.001	0.622
getTitle-methods	0.658	0.001	0.659
getType-methods	1.090	0.001	1.092
graphDensity	0.003	0.000	0.004
isHomoList	0.001	0.000	0.001
mergeKEGGgraphs	3.315	0.003	3.318
neighborhood	0.022	0.000	0.022
parseKGML	0.695	0.004	0.699
parseKGML2Graph	1.692	0.002	1.694
plotKEGGgraph	3.443	0.010	3.453
pvalue2asterisk	0.001	0.000	0.000
queryKEGGsubgraph	1.755	0.001	1.758
randomSubGraph	0.034	0.000	0.034
splitKEGGgroup	0.691	0.002	0.692
subGraphByNodeType	1.711	0.002	1.713
subKEGGgraph	1.793	0.003	1.795
translateKEGGID2GeneID	0.001	0.000	0.000
translateKEGGgraph	1.767	0.001	1.769