Package: KEGGgraph

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/2.11/Resources/bin/R CMD check --no-vignettes --timings KEGGgraph_1.4.0.tar.gz

StartedAt: 2010-10-04 17:32:38 -0700 (Mon, 04 Oct 2010)

EndedAt: 2010-10-04 17:35:05 -0700 (Mon, 04 Oct 2010)

EllapsedTime: 147.2 seconds

RetCode: 0

Status:  OK

CheckDir: KEGGgraph.Rcheck

Warnings: 0

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.6-bioc/meat/KEGGgraph.Rcheck'
* using R version 2.11.1 Patched (2010-05-31 r52167)
* using session charset: UTF-8
* 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 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 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	2.025	0.015	2.048
KEGGEdgeSubType-class	0.002	0.001	0.001
KEGGEdgeSubtype	0.015	0.002	0.017
KEGGGraphics-class	0.001	0.001	0.002
KEGGGroup-class	0.002	0.000	0.002
KEGGNode-class	1.232	0.007	1.250
KEGGPathway-class	1.942	0.012	1.973
KEGGPathwayInfo-class	1.196	0.006	1.218
KEGGReaction-class	2.038	0.011	2.068
KEGGpathway2Graph	1.326	0.008	1.340
KEGGpathway2reactionGraph	2.040	0.010	2.065
expandKEGGPathway	2.579	0.009	2.609
getDisplayName-methods	1.200	0.006	1.209
getEntryID-methods	1.214	0.006	1.225
getKEGGID-methods	0.607	0.004	0.613
getKEGGgeneLink-methods	0.000	0.000	0.001
getKEGGnodeData	3.130	0.012	3.160
getKGMLurl	0.008	0.019	0.028
getName-methods	1.154	0.024	1.197
getNamedElement	0.001	0.000	0.001
getPathwayInfo-methods	1.157	0.008	1.218
getReactions-methods	1.913	0.016	1.948
getRgraphvizEdgeNames	0.005	0.000	0.005
getSubtype-methods	1.165	0.005	1.188
getTitle-methods	1.142	0.004	1.156
getType-methods	1.921	0.005	1.949
graphDensity	0.007	0.000	0.007
isHomoList	0.001	0.001	0.002
mergeKEGGgraphs	5.487	0.017	5.553
neighborhood	0.056	0.001	0.057
parseKGML	1.276	0.004	1.280
parseKGML2Graph	3.299	0.006	3.326
plotKEGGgraph	5.735	0.025	5.807
pvalue2asterisk	0.001	0.000	0.001
queryKEGGsubgraph	2.938	0.010	2.966
randomSubGraph	0.063	0.000	0.064
splitKEGGgroup	1.179	0.005	1.193
subGraphByNodeType	3.085	0.013	3.112
subKEGGgraph	3.081	0.013	3.113
translateKEGGID2GeneID	0.001	0.001	0.001
translateKEGGgraph	3.244	0.014	3.280