Package: KEGGgraph

Version: 1.4.0

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

StartedAt: 2010-10-04 17:23:41 -0700 (Mon, 04 Oct 2010)

EndedAt: 2010-10-04 17:25:42 -0700 (Mon, 04 Oct 2010)

EllapsedTime: 121.0 seconds

RetCode: 0

Status:  OK

CheckDir: KEGGgraph.Rcheck

Warnings: 0

* checking for working pdflatex ... OK
* using log directory 'D:/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	1.47	0.00	1.49
KEGGEdgeSubType-class	0	0	0
KEGGEdgeSubtype	0.02	0.00	0.01
KEGGGraphics-class	0	0	0
KEGGGroup-class	0	0	0
KEGGNode-class	0.90	0.00	0.91
KEGGPathway-class	1.43	0.00	1.42
KEGGPathwayInfo-class	0.84	0.00	0.84
KEGGReaction-class	1.40	0.00	1.39
KEGGpathway2Graph	1.15	0.00	1.16
KEGGpathway2reactionGraph	1.36	0.00	1.36
expandKEGGPathway	1.92	0.00	1.92
getDisplayName-methods	1.03	0.00	1.03
getEntryID-methods	0.86	0.00	0.86
getKEGGID-methods	0.39	0.02	0.41
getKEGGgeneLink-methods	0	0	0
getKEGGnodeData	2.19	0.00	2.19
getKGMLurl	0	0	0
getName-methods	0.92	0.00	0.92
getNamedElement	0	0	0
getPathwayInfo-methods	0.96	0.00	0.96
getReactions-methods	1.29	0.00	1.29
getRgraphvizEdgeNames	0	0	0
getSubtype-methods	0.83	0.00	0.83
getTitle-methods	0.84	0.00	0.84
getType-methods	1.44	0.00	1.44
graphDensity	0.02	0.00	0.02
isHomoList	0	0	0
mergeKEGGgraphs	4.1	0.0	4.1
neighborhood	0.04	0.00	0.04
parseKGML	0.9	0.0	0.9
parseKGML2Graph	2.1	0.0	2.1
plotKEGGgraph	4.15	0.00	4.15
pvalue2asterisk	0	0	0
queryKEGGsubgraph	2.36	0.00	2.36
randomSubGraph	0.05	0.00	0.05
splitKEGGgroup	0.87	0.00	0.87
subGraphByNodeType	2.03	0.00	2.03
subKEGGgraph	2.4	0.0	2.4
translateKEGGID2GeneID	0	0	0
translateKEGGgraph	2.1	0.0	2.1