Package: KEGGgraph

Version: 1.9.0

Command: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings KEGGgraph_1.9.0.tar.gz

StartedAt: 2011-05-09 17:50:26 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 17:52:51 -0700 (Mon, 09 May 2011)

EllapsedTime: 144.6 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 2.14.0 Under development (unstable) (2011-04-17 r55484)
* 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 '1.9.0'
* 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 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 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
Warning in fun(...) :
  Rgraphviz built with Graphviz version 2.20.3.
Found installed Graphviz version 2.25.20090912.445. This _may_ cause problems.
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'KEGGgraph.Rnw' 
   'KEGGgraphApp.Rnw' 
** testing if installed package can be loaded
Warning message:
In fun(...) : Rgraphviz built with Graphviz version 2.20.3.
Found installed Graphviz version 2.25.20090912.445. This _may_ cause problems.

* DONE (KEGGgraph)

name	user	system	elapsed
KEGGEdge-class	1.11	0.00	1.11
KEGGEdgeSubType-class	0	0	0
KEGGEdgeSubtype	0.01	0.00	0.02
KEGGGraphics-class	0	0	0
KEGGGroup-class	0	0	0
KEGGNode-class	0.66	0.00	0.65
KEGGPathway-class	1.11	0.00	1.11
KEGGPathwayInfo-class	0.58	0.00	0.58
KEGGReaction-class	1.03	0.00	1.03
KEGGpathway2Graph	0.81	0.00	0.81
KEGGpathway2reactionGraph	1.20	0.00	1.21
expandKEGGPathway	1.50	0.02	1.51
getDisplayName-methods	0.66	0.00	0.66
getEntryID-methods	0.63	0.00	0.62
getKEGGID-methods	0.29	0.00	0.30
getKEGGgeneLink-methods	0	0	0
getKEGGnodeData	1.61	0.00	1.60
getKGMLurl	0.00	0.01	0.04
getName-methods	0.65	0.00	0.65
getNamedElement	0	0	0
getPathwayInfo-methods	0.72	0.00	0.72
getReactions-methods	0.96	0.00	0.95
getRgraphvizEdgeNames	0	0	0
getSubtype-methods	0.60	0.00	0.61
getTitle-methods	0.6	0.0	0.6
getType-methods	1.06	0.00	1.06
graphDensity	0.02	0.00	0.02
isHomoList	0	0	0
mergeKEGGgraphs	3.29	0.00	3.29
neighborhood	0.02	0.00	0.02
parseKGML	0.71	0.00	0.71
parseKGML2Graph	1.54	0.00	1.54
plotKEGGgraph	3.5	0.0	3.5
pvalue2asterisk	0	0	0
queryKEGGsubgraph	1.6	0.0	1.6
randomSubGraph	0.03	0.00	0.03
splitKEGGgroup	0.59	0.00	0.59
subGraphByNodeType	1.64	0.00	1.64
subKEGGgraph	1.57	0.00	1.57
translateKEGGID2GeneID	0	0	0
translateKEGGgraph	1.67	0.00	1.67