BioC 2.12: CHECK report for KEGGgraph on petty

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: 2013-10-08 22:53:37 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 22:56:24 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 166.5 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 3.0.1 (2013-05-16)
* 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 ... [7s/8s] 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 ... [52s/53s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
plotKEGGgraph 5.199  0.027   5.263
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'kegg2graph.R' [24s/25s]
  Running 'testGraph.R' [3s/3s]
 [28s/28s] 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	1.423	0.017	1.474
KEGGEdgeSubType-class	0.008	0.000	0.009
KEGGEdgeSubtype	0.028	0.002	0.030
KEGGGraphics-class	0.011	0.001	0.012
KEGGGroup-class	0.008	0.000	0.009
KEGGNode-class	0.778	0.013	0.833
KEGGPathway-class	1.283	0.011	1.328
KEGGPathwayInfo-class	0.779	0.008	0.797
KEGGReaction-class	1.372	0.013	1.406
KEGGpathway2Graph	0.942	0.006	0.966
KEGGpathway2reactionGraph	1.382	0.013	1.401
expandKEGGPathway	1.949	0.006	1.960
getDisplayName-methods	1.023	0.012	1.036
getEntryID-methods	0.788	0.007	0.797
getKEGGID-methods	0.429	0.003	0.435
getKEGGgeneLink-methods	0.012	0.000	0.013
getKEGGnodeData	2.525	0.008	2.539
getKGMLurl	0.018	0.002	0.022
getName-methods	0.866	0.017	0.885
getNamedElement	0.008	0.000	0.008
getPathwayInfo-methods	0.775	0.005	0.790
getReactions-methods	1.268	0.013	1.293
getRgraphvizEdgeNames	0.014	0.000	0.015
getSubtype-methods	0.782	0.004	0.790
getTitle-methods	0.818	0.005	0.832
getType-methods	1.320	0.010	1.337
graphDensity	0.017	0.000	0.016
isHomoList	0.008	0.000	0.009
mergeKEGGgraphs	4.499	0.034	4.632
neighborhood	0.419	0.010	0.432
parseKGML	0.781	0.004	0.791
parseKGML2DataFrame	3.467	0.015	3.546
parseKGML2Graph	2.279	0.011	2.324
plotKEGGgraph	5.199	0.027	5.263
pvalue2asterisk	0.025	0.000	0.026
queryKEGGsubgraph	2.368	0.011	2.385
randomSubGraph	0.061	0.001	0.061
splitKEGGgroup	0.883	0.005	0.893
subGraphByNodeType	2.523	0.008	2.645
subKEGGgraph	2.303	0.009	2.391
translateKEGGID2GeneID	0.013	0.000	0.016
translateKEGGgraph	2.674	0.009	2.709