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: 2013-03-25 03:16:58 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 03:19:11 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 133.1 seconds

RetCode: 0

Status:  OK

CheckDir: KEGGgraph.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/KEGGgraph.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* 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 '1.15.0'
* 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 ... [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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [44s/44s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'kegg2graph.R' [21s/21s]
  Running 'testGraph.R' [3s/3s]
 [24s/24s] 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	1.357	0.027	1.385
KEGGEdgeSubType-class	0.007	0.005	0.013
KEGGEdgeSubtype	0.017	0.009	0.026
KEGGGraphics-class	0.006	0.005	0.011
KEGGGroup-class	0.007	0.005	0.012
KEGGNode-class	0.553	0.019	0.575
KEGGPathway-class	0.876	0.024	0.901
KEGGPathwayInfo-class	0.628	0.013	0.644
KEGGReaction-class	1.260	0.022	1.284
KEGGpathway2Graph	0.918	0.013	0.931
KEGGpathway2reactionGraph	1.312	0.017	1.329
expandKEGGPathway	1.880	0.015	1.897
getDisplayName-methods	0.770	0.016	0.787
getEntryID-methods	0.784	0.021	0.805
getKEGGID-methods	0.406	0.013	0.420
getKEGGgeneLink-methods	0.013	0.007	0.019
getKEGGnodeData	2.267	0.016	2.283
getKGMLurl	0.023	0.021	0.045
getName-methods	0.806	0.040	0.846
getNamedElement	0.014	0.010	0.029
getPathwayInfo-methods	0.819	0.028	0.847
getReactions-methods	1.255	0.015	1.271
getRgraphvizEdgeNames	0.014	0.008	0.021
getSubtype-methods	0.768	0.014	0.782
getTitle-methods	0.770	0.014	0.784
getType-methods	1.316	0.019	1.334
graphDensity	0.014	0.008	0.023
isHomoList	0.013	0.009	0.022
mergeKEGGgraphs	4.050	0.026	4.080
neighborhood	0.462	0.029	0.493
parseKGML	0.605	0.012	0.617
parseKGML2DataFrame	2.917	0.022	2.940
parseKGML2Graph	1.793	0.012	1.806
plotKEGGgraph	3.063	0.023	3.087
pvalue2asterisk	0.012	0.007	0.019
queryKEGGsubgraph	2.109	0.024	2.136
randomSubGraph	0.052	0.009	0.061
splitKEGGgroup	0.593	0.013	0.607
subGraphByNodeType	1.581	0.011	1.592
subKEGGgraph	1.831	0.013	1.845
translateKEGGID2GeneID	0.010	0.007	0.017
translateKEGGgraph	1.800	0.022	1.826