Package: KEGGgraph

Version: 1.4.0

Command: E:\biocbld\bbs-2.6-bioc\R\bin\R.exe CMD check --no-vignettes --timings KEGGgraph_1.4.0.tar.gz

StartedAt: 2010-10-04 18:48:48 -0700 (Mon, 04 Oct 2010)

EndedAt: 2010-10-04 18:50:58 -0700 (Mon, 04 Oct 2010)

EllapsedTime: 129.6 seconds

RetCode: 0

Status:  OK

CheckDir: KEGGgraph.Rcheck

Warnings: 0

* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.6-bioc/meat/KEGGgraph.Rcheck'
* using R version 2.11.1 (2010-05-31)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'KEGGgraph/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'KEGGgraph' version '1.4.0'
* 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 data for non-ASCII characters ... OK
* checking examples ... OK
* checking tests ...
  Running 'kegg2graph.R'
  Running 'testGraph.R'
 OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

* install options are ' --no-html'

* 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	1.43	0.00	1.44
KEGGEdgeSubType-class	0	0	0
KEGGEdgeSubtype	0.00	0.01	0.01
KEGGGraphics-class	0	0	0
KEGGGroup-class	0	0	0
KEGGNode-class	0.81	0.00	0.81
KEGGPathway-class	1.24	0.00	1.26
KEGGPathwayInfo-class	0.84	0.02	0.86
KEGGReaction-class	1.31	0.00	1.31
KEGGpathway2Graph	0.96	0.01	0.99
KEGGpathway2reactionGraph	1.42	0.00	1.42
expandKEGGPathway	1.84	0.00	1.85
getDisplayName-methods	0.78	0.00	0.79
getEntryID-methods	0.86	0.00	0.85
getKEGGID-methods	0.42	0.00	0.42
getKEGGgeneLink-methods	0	0	0
getKEGGnodeData	2.19	0.00	2.19
getKGMLurl	0.00	0.02	0.06
getName-methods	0.86	0.00	0.86
getNamedElement	0	0	0
getPathwayInfo-methods	0.92	0.00	0.92
getReactions-methods	1.41	0.00	1.41
getRgraphvizEdgeNames	0	0	0
getSubtype-methods	0.75	0.00	0.75
getTitle-methods	0.8	0.0	0.8
getType-methods	1.33	0.00	1.33
graphDensity	0.01	0.00	0.02
isHomoList	0	0	0
mergeKEGGgraphs	3.97	0.02	3.98
neighborhood	0.03	0.00	0.03
parseKGML	0.83	0.02	0.85
parseKGML2Graph	1.97	0.00	2.00
plotKEGGgraph	4.01	0.01	4.03
pvalue2asterisk	0	0	0
queryKEGGsubgraph	2.08	0.02	2.09
randomSubGraph	0.05	0.00	0.05
splitKEGGgroup	0.87	0.00	0.87
subGraphByNodeType	1.94	0.00	1.96
subKEGGgraph	2.28	0.01	2.29
translateKEGGID2GeneID	0	0	0
translateKEGGgraph	2.02	0.02	2.03