Package: KEGGgraph

Version: 1.13.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch KEGGgraph_1.13.0.tar.gz

StartedAt: 2012-06-21 01:11:34 -0700 (Thu, 21 Jun 2012)

EndedAt: 2012-06-21 01:13:50 -0700 (Thu, 21 Jun 2012)

EllapsedTime: 135.4 seconds

RetCode: 0

Status:  OK

CheckDir: KEGGgraph.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/KEGGgraph.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'KEGGgraph/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'KEGGgraph' version '1.13.0'
* 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 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 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'kegg2graph.R'
  Running 'testGraph.R'
 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-2.11-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	1.173	0.013	1.189
KEGGEdgeSubType-class	0.001	0.001	0.001
KEGGEdgeSubtype	0.017	0.003	0.023
KEGGGraphics-class	0.001	0.000	0.001
KEGGGroup-class	0.001	0.000	0.002
KEGGNode-class	0.663	0.006	0.675
KEGGPathway-class	1.138	0.009	1.160
KEGGPathwayInfo-class	0.626	0.004	0.631
KEGGReaction-class	1.131	0.008	1.146
KEGGpathway2Graph	0.773	0.008	0.790
KEGGpathway2reactionGraph	1.128	0.007	1.139
expandKEGGPathway	1.568	0.007	1.577
getDisplayName-methods	0.700	0.004	0.709
getEntryID-methods	0.614	0.004	0.624
getKEGGID-methods	0.323	0.003	0.326
getKEGGgeneLink-methods	0.001	0.000	0.000
getKEGGnodeData	1.879	0.007	1.891
getKGMLurl	0.005	0.010	0.017
getName-methods	0.698	0.029	0.730
getNamedElement	0.001	0.000	0.000
getPathwayInfo-methods	0.624	0.005	0.631
getReactions-methods	1.047	0.006	1.085
getRgraphvizEdgeNames	0.003	0.000	0.003
getSubtype-methods	0.640	0.004	0.650
getTitle-methods	0.648	0.003	0.653
getType-methods	1.177	0.004	1.185
graphDensity	0.003	0.000	0.004
isHomoList	0.001	0.001	0.001
mergeKEGGgraphs	3.756	0.016	3.790
neighborhood	0.555	0.018	0.578
parseKGML	0.622	0.004	0.629
parseKGML2DataFrame	2.877	0.013	2.912
parseKGML2Graph	2.091	0.011	2.106
plotKEGGgraph	3.908	0.021	3.939
pvalue2asterisk	0.000	0.001	0.001
queryKEGGsubgraph	2.030	0.008	2.054
randomSubGraph	0.043	0.001	0.045
splitKEGGgroup	0.731	0.005	0.749
subGraphByNodeType	1.877	0.006	1.893
subKEGGgraph	2.078	0.007	2.095
translateKEGGID2GeneID	0.001	0.000	0.001
translateKEGGgraph	1.869	0.011	1.889