Package: KEGGgraph

Version: 1.16.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch KEGGgraph_1.16.0.tar.gz

StartedAt: 2013-05-01 07:17:19 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 07:19:50 -0700 (Wed, 01 May 2013)

EllapsedTime: 151.1 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 Patched (2013-04-08 r62531)
* 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 '1.16.0'
* 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 ... [6s/6s] 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 ... [45s/46s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'kegg2graph.R' [22s/23s]
  Running 'testGraph.R' [3s/3s]
 [26s/27s] 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
** testing if installed package can be loaded
* DONE (KEGGgraph)

name	user	system	elapsed
KEGGEdge-class	1.275	0.022	1.324
KEGGEdgeSubType-class	0.016	0.002	0.020
KEGGEdgeSubtype	0.030	0.002	0.032
KEGGGraphics-class	0.008	0.001	0.009
KEGGGroup-class	0.011	0.001	0.011
KEGGNode-class	0.652	0.023	0.695
KEGGPathway-class	1.111	0.023	1.170
KEGGPathwayInfo-class	0.655	0.008	0.669
KEGGReaction-class	1.111	0.008	1.122
KEGGpathway2Graph	0.735	0.017	0.763
KEGGpathway2reactionGraph	1.109	0.014	1.149
expandKEGGPathway	1.571	0.015	1.612
getDisplayName-methods	0.740	0.012	0.778
getEntryID-methods	0.633	0.017	0.660
getKEGGID-methods	0.360	0.017	0.450
getKEGGgeneLink-methods	0.011	0.000	0.011
getKEGGnodeData	1.886	0.021	1.964
getKGMLurl	0.207	0.006	0.228
getName-methods	0.657	0.011	0.695
getNamedElement	0.020	0.001	0.021
getPathwayInfo-methods	0.668	0.010	0.693
getReactions-methods	1.097	0.014	1.137
getRgraphvizEdgeNames	0.020	0.001	0.022
getSubtype-methods	0.666	0.008	0.694
getTitle-methods	0.796	0.010	0.807
getType-methods	1.068	0.011	1.095
graphDensity	0.016	0.001	0.019
isHomoList	0.015	0.002	0.017
mergeKEGGgraphs	3.782	0.053	3.948
neighborhood	0.349	0.015	0.373
parseKGML	0.702	0.020	0.759
parseKGML2DataFrame	2.975	0.025	3.096
parseKGML2Graph	2.096	0.024	2.195
plotKEGGgraph	4.296	0.052	4.438
pvalue2asterisk	0.031	0.002	0.033
queryKEGGsubgraph	1.976	0.026	2.036
randomSubGraph	0.059	0.002	0.062
splitKEGGgroup	0.775	0.008	0.800
subGraphByNodeType	2.135	0.023	2.203
subKEGGgraph	2.055	0.019	2.137
translateKEGGID2GeneID	0.014	0.001	0.015
translateKEGGgraph	2.384	0.023	2.445