Package: KEGGgraph

Version: 1.14.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch KEGGgraph_1.14.0.tar.gz

StartedAt: 2013-03-25 00:10:51 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 00:12:38 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 106.9 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 2.15.3 (2013-03-01)
* 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 '1.14.0'
* 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 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 ... 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	0.856	0.013	0.877
KEGGEdgeSubType-class	0.001	0.000	0.001
KEGGEdgeSubtype	0.008	0.001	0.015
KEGGGraphics-class	0.000	0.000	0.001
KEGGGroup-class	0.001	0.001	0.001
KEGGNode-class	0.524	0.006	0.531
KEGGPathway-class	0.798	0.009	0.813
KEGGPathwayInfo-class	0.488	0.004	0.493
KEGGReaction-class	0.829	0.008	0.856
KEGGpathway2Graph	0.580	0.010	0.607
KEGGpathway2reactionGraph	0.861	0.007	0.871
expandKEGGPathway	1.195	0.006	1.208
getDisplayName-methods	0.584	0.004	0.599
getEntryID-methods	0.455	0.003	0.459
getKEGGID-methods	0.243	0.003	0.247
getKEGGgeneLink-methods	0	0	0
getKEGGnodeData	1.433	0.008	1.447
getKGMLurl	0.004	0.013	0.018
getName-methods	0.565	0.021	0.587
getNamedElement	0	0	0
getPathwayInfo-methods	0.645	0.014	0.666
getReactions-methods	0.754	0.005	0.764
getRgraphvizEdgeNames	0.002	0.001	0.002
getSubtype-methods	0.465	0.005	0.471
getTitle-methods	0.484	0.005	0.488
getType-methods	0.796	0.005	0.803
graphDensity	0.003	0.000	0.003
isHomoList	0.001	0.000	0.001
mergeKEGGgraphs	2.862	0.020	2.896
neighborhood	0.280	0.015	0.306
parseKGML	0.583	0.005	0.593
parseKGML2DataFrame	2.139	0.011	2.157
parseKGML2Graph	1.497	0.006	1.509
plotKEGGgraph	3.033	0.017	3.058
pvalue2asterisk	0.000	0.000	0.001
queryKEGGsubgraph	1.470	0.008	1.484
randomSubGraph	0.028	0.000	0.028
splitKEGGgroup	0.512	0.004	0.517
subGraphByNodeType	1.590	0.006	1.598
subKEGGgraph	1.342	0.007	1.351
translateKEGGID2GeneID	0	0	0
translateKEGGgraph	1.542	0.016	1.559