Package: KEGGgraph

Version: 1.15.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch KEGGgraph_1.15.0.tar.gz

StartedAt: 2013-03-24 06:59:35 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 07:02:07 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 152.3 seconds

RetCode: 0

Status:  OK

CheckDir: KEGGgraph.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/KEGGgraph.Rcheck'
* using R version 3.0.0 beta (2013-03-21 r62346)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'KEGGgraph/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'KEGGgraph' version '1.15.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'KEGGgraph' can be installed ... [7s/7s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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 installed files from 'inst/doc' ... OK
* checking examples ... [44s/45s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'kegg2graph.R' [22s/22s]
  Running 'testGraph.R' [3s/3s]
 [25s/26s] OK
* checking for unstated dependencies in vignettes ... OK
* 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

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/KEGGgraph.Rcheck/00check.log'
for details.

* installing *source* package 'KEGGgraph' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'KEGGgraph.Rnw' 
   'KEGGgraphApp.Rnw' 
** testing if installed package can be loaded
* DONE (KEGGgraph)

name	user	system	elapsed
KEGGEdge-class	1.246	0.024	1.272
KEGGEdgeSubType-class	0.013	0.001	0.014
KEGGEdgeSubtype	0.147	0.003	0.150
KEGGGraphics-class	0.010	0.001	0.011
KEGGGroup-class	0.012	0.001	0.013
KEGGNode-class	0.653	0.019	0.673
KEGGPathway-class	1.205	0.013	1.219
KEGGPathwayInfo-class	0.718	0.006	0.728
KEGGReaction-class	1.051	0.022	1.078
KEGGpathway2Graph	0.822	0.008	0.831
KEGGpathway2reactionGraph	1.129	0.011	1.141
expandKEGGPathway	1.856	0.013	1.873
getDisplayName-methods	0.703	0.009	0.713
getEntryID-methods	0.651	0.007	0.660
getKEGGID-methods	0.378	0.008	0.392
getKEGGgeneLink-methods	0.010	0.001	0.011
getKEGGnodeData	2.202	0.023	2.235
getKGMLurl	0.025	0.003	0.030
getName-methods	0.712	0.013	0.729
getNamedElement	0.013	0.002	0.014
getPathwayInfo-methods	0.697	0.010	0.712
getReactions-methods	0.977	0.010	0.989
getRgraphvizEdgeNames	0.021	0.000	0.021
getSubtype-methods	0.749	0.010	0.767
getTitle-methods	0.720	0.011	0.734
getType-methods	1.237	0.023	1.265
graphDensity	0.012	0.001	0.013
isHomoList	0.011	0.002	0.012
mergeKEGGgraphs	3.677	0.037	3.728
neighborhood	0.507	0.016	0.527
parseKGML	0.643	0.014	0.662
parseKGML2DataFrame	2.860	0.037	2.911
parseKGML2Graph	2.066	0.012	2.083
plotKEGGgraph	3.791	0.035	3.839
pvalue2asterisk	0.020	0.002	0.021
queryKEGGsubgraph	1.993	0.018	2.014
randomSubGraph	0.045	0.001	0.045
splitKEGGgroup	0.666	0.004	0.671
subGraphByNodeType	2.115	0.013	2.130
subKEGGgraph	2.174	0.016	2.194
translateKEGGID2GeneID	0.013	0.001	0.015
translateKEGGgraph	1.877	0.017	1.906