Package: KEGGgraph

Version: 1.6.0

Command: E:\biocbld\bbs-2.7-bioc\R\bin\R.exe CMD check --no-vignettes --timings KEGGgraph_1.6.0.tar.gz

StartedAt: 2011-04-07 07:34:41 -0700 (Thu, 07 Apr 2011)

EndedAt: 2011-04-07 07:36:36 -0700 (Thu, 07 Apr 2011)

EllapsedTime: 114.8 seconds

RetCode: 0

Status:  OK

CheckDir: KEGGgraph.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.7-bioc/meat/KEGGgraph.Rcheck'
* using R version 2.12.2 (2011-02-25)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* 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 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	1.19	0.01	1.22
KEGGEdgeSubType-class	0	0	0
KEGGEdgeSubtype	0.00	0.00	0.02
KEGGGraphics-class	0	0	0
KEGGGroup-class	0	0	0
KEGGNode-class	0.62	0.00	0.63
KEGGPathway-class	1.17	0.00	1.17
KEGGPathwayInfo-class	0.64	0.00	0.64
KEGGReaction-class	1.17	0.00	1.17
KEGGpathway2Graph	0.80	0.00	0.85
KEGGpathway2reactionGraph	1.24	0.00	1.25
expandKEGGPathway	1.84	0.00	1.86
getDisplayName-methods	0.73	0.02	0.75
getEntryID-methods	0.60	0.00	0.59
getKEGGID-methods	0.33	0.00	0.33
getKEGGgeneLink-methods	0	0	0
getKEGGnodeData	2.17	0.00	2.19
getKGMLurl	0.00	0.00	0.11
getName-methods	0.72	0.00	0.72
getNamedElement	0	0	0
getPathwayInfo-methods	0.73	0.01	0.75
getReactions-methods	1.27	0.02	1.32
getRgraphvizEdgeNames	0	0	0
getSubtype-methods	0.65	0.00	0.66
getTitle-methods	0.61	0.00	0.64
getType-methods	1.16	0.00	1.17
graphDensity	0	0	0
isHomoList	0.02	0.00	0.02
mergeKEGGgraphs	4.23	0.00	4.31
neighborhood	0.03	0.00	0.03
parseKGML	0.70	0.00	0.71
parseKGML2Graph	2.16	0.00	2.17
plotKEGGgraph	5.17	0.00	5.20
pvalue2asterisk	0	0	0
queryKEGGsubgraph	2.28	0.02	2.30
randomSubGraph	0.05	0.00	0.04
splitKEGGgroup	0.73	0.00	0.74
subGraphByNodeType	2.11	0.00	2.11
subKEGGgraph	2.38	0.00	2.39
translateKEGGID2GeneID	0	0	0
translateKEGGgraph	2.23	0.00	2.26