Package: KEGGgraph

Version: 1.9.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch KEGGgraph_1.9.0.tar.gz

StartedAt: 2011-06-22 03:44:20 -0700 (Wed, 22 Jun 2011)

EndedAt: 2011-06-22 03:46:35 -0700 (Wed, 22 Jun 2011)

EllapsedTime: 135.7 seconds

RetCode: 0

Status:  OK

CheckDir: KEGGgraph.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/KEGGgraph.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-03 r56037)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘KEGGgraph/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘KEGGgraph’ version ‘1.9.0’
* 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 installed package size ... 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 for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... 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 for unstated dependencies in vignettes ... NOTE
‘library’ or ‘require’ call not declared from: ‘RColorBrewer’
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... 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 ...
*** tangling vignette sources ...
   ‘KEGGgraph.Rnw’ 
   ‘KEGGgraphApp.Rnw’ 
** testing if installed package can be loaded

* DONE (KEGGgraph)

name	user	system	elapsed
KEGGEdge-class	1.520	0.016	1.550
KEGGEdgeSubType-class	0.001	0.001	0.001
KEGGEdgeSubtype	0.011	0.002	0.013
KEGGGraphics-class	0.002	0.000	0.002
KEGGGroup-class	0.002	0.000	0.002
KEGGNode-class	0.866	0.006	0.886
KEGGPathway-class	1.418	0.009	1.453
KEGGPathwayInfo-class	0.883	0.010	0.914
KEGGReaction-class	1.373	0.006	1.397
KEGGpathway2Graph	1.018	0.006	1.035
KEGGpathway2reactionGraph	1.489	0.008	1.515
expandKEGGPathway	1.975	0.009	2.013
getDisplayName-methods	0.989	0.005	1.001
getEntryID-methods	0.827	0.005	0.839
getKEGGID-methods	0.429	0.004	0.444
getKEGGgeneLink-methods	0.001	0.000	0.000
getKEGGnodeData	2.299	0.011	2.329
getKGMLurl	0.008	0.018	0.028
getName-methods	0.940	0.022	0.975
getNamedElement	0.001	0.000	0.001
getPathwayInfo-methods	0.923	0.014	0.969
getReactions-methods	1.404	0.013	1.474
getRgraphvizEdgeNames	0.004	0.001	0.004
getSubtype-methods	0.863	0.010	0.904
getTitle-methods	0.826	0.004	0.842
getType-methods	1.437	0.010	1.520
graphDensity	0.004	0.000	0.005
isHomoList	0.001	0.000	0.001
mergeKEGGgraphs	4.407	0.019	4.479
neighborhood	0.030	0.001	0.031
parseKGML	0.892	0.003	0.895
parseKGML2Graph	2.209	0.006	2.216
plotKEGGgraph	4.629	0.025	4.686
pvalue2asterisk	0.001	0.000	0.001
queryKEGGsubgraph	2.412	0.007	2.422
randomSubGraph	0.045	0.000	0.045
splitKEGGgroup	0.822	0.003	0.826
subGraphByNodeType	2.303	0.008	2.314
subKEGGgraph	2.476	0.008	2.486
translateKEGGID2GeneID	0.001	0.000	0.001
translateKEGGgraph	2.287	0.010	2.301