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: 2011-03-31 07:03:11 -0700 (Thu, 31 Mar 2011)

EndedAt: 2011-03-31 07:05:05 -0700 (Thu, 31 Mar 2011)

EllapsedTime: 114.4 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	1.2	0.0	1.2
KEGGEdgeSubType-class	0	0	0
KEGGEdgeSubtype	0.02	0.00	0.01
KEGGGraphics-class	0	0	0
KEGGGroup-class	0	0	0
KEGGNode-class	0.67	0.00	0.68
KEGGPathway-class	1.14	0.00	1.14
KEGGPathwayInfo-class	0.66	0.00	0.65
KEGGReaction-class	1.21	0.00	1.22
KEGGpathway2Graph	0.8	0.0	0.8
KEGGpathway2reactionGraph	1.25	0.00	1.25
expandKEGGPathway	1.97	0.00	1.97
getDisplayName-methods	0.77	0.00	0.76
getEntryID-methods	0.62	0.00	0.63
getKEGGID-methods	0.31	0.02	0.33
getKEGGgeneLink-methods	0	0	0
getKEGGnodeData	2.19	0.01	2.21
getKGMLurl	0.00	0.00	0.06
getName-methods	0.71	0.02	0.73
getNamedElement	0	0	0
getPathwayInfo-methods	0.77	0.00	0.77
getReactions-methods	1.34	0.00	1.40
getRgraphvizEdgeNames	0	0	0
getSubtype-methods	0.64	0.00	0.64
getTitle-methods	0.68	0.00	0.68
getType-methods	1.15	0.00	1.17
graphDensity	0	0	0
isHomoList	0	0	0
mergeKEGGgraphs	4.41	0.00	4.40
neighborhood	0.03	0.00	0.04
parseKGML	0.73	0.00	0.73
parseKGML2Graph	2.11	0.02	2.13
plotKEGGgraph	5.33	0.01	5.35
pvalue2asterisk	0	0	0
queryKEGGsubgraph	2.17	0.00	2.19
randomSubGraph	0.04	0.00	0.03
splitKEGGgroup	0.75	0.02	0.77
subGraphByNodeType	2.25	0.00	2.25
subKEGGgraph	2.13	0.00	2.13
translateKEGGID2GeneID	0	0	0
translateKEGGgraph	2.29	0.00	2.30