Package: KEGGgraph

Version: 1.10.0

Command: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch KEGGgraph_1.10.0.tar.gz

StartedAt: 2012-01-09 03:51:52 -0800 (Mon, 09 Jan 2012)

EndedAt: 2012-01-09 03:53:28 -0800 (Mon, 09 Jan 2012)

EllapsedTime: 96.0 seconds

RetCode: 0

Status:  OK

CheckDir: KEGGgraph.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/KEGGgraph.Rcheck'
* using R version 2.14.1 (2011-12-22)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'KEGGgraph/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'KEGGgraph' version '1.10.0'
* 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 whether package 'KEGGgraph' can be installed ... OK
* checking installed package size ... 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 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 ... NOTE
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                             old_size new_size compress
  colorectalcancerSPIA.RData    955Kb    832Kb       xz
* 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
** 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	0.94	0.01	0.95
KEGGEdgeSubType-class	0	0	0
KEGGEdgeSubtype	0.02	0.00	0.02
KEGGGraphics-class	0	0	0
KEGGGroup-class	0	0	0
KEGGNode-class	0.53	0.00	0.53
KEGGPathway-class	0.83	0.00	0.83
KEGGPathwayInfo-class	0.62	0.00	0.62
KEGGReaction-class	0.85	0.00	0.85
KEGGpathway2Graph	0.59	0.00	0.59
KEGGpathway2reactionGraph	0.89	0.00	0.89
expandKEGGPathway	1.25	0.00	1.25
getDisplayName-methods	0.54	0.00	0.54
getEntryID-methods	0.57	0.00	0.57
getKEGGID-methods	0.25	0.00	0.25
getKEGGgeneLink-methods	0	0	0
getKEGGnodeData	1.51	0.00	1.51
getKGMLurl	0.02	0.00	0.02
getName-methods	0.68	0.00	0.69
getNamedElement	0	0	0
getPathwayInfo-methods	0.47	0.00	0.46
getReactions-methods	0.84	0.00	0.84
getRgraphvizEdgeNames	0	0	0
getSubtype-methods	0.44	0.00	0.44
getTitle-methods	0.52	0.00	0.52
getType-methods	0.81	0.00	0.81
graphDensity	0.01	0.00	0.02
isHomoList	0	0	0
mergeKEGGgraphs	3.00	0.02	3.01
neighborhood	0.28	0.01	0.30
parseKGML	0.60	0.00	0.59
parseKGML2DataFrame	2.37	0.00	2.38
parseKGML2Graph	1.43	0.00	1.42
plotKEGGgraph	2.92	0.00	2.92
pvalue2asterisk	0	0	0
queryKEGGsubgraph	1.62	0.00	1.63
randomSubGraph	0.02	0.00	0.02
splitKEGGgroup	0.48	0.00	0.48
subGraphByNodeType	1.64	0.00	1.64
subKEGGgraph	1.42	0.00	1.42
translateKEGGID2GeneID	0	0	0
translateKEGGgraph	1.46	0.00	1.46