Package: KEGGgraph

Version: 1.8.0

Command: /home/biocbuild/bbs-2.8-bioc/R/bin/R CMD check --no-vignettes --timings KEGGgraph_1.8.0.tar.gz

StartedAt: 2011-10-20 13:15:16 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 13:16:57 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 100.8 seconds

RetCode: 0

Status:  OK

CheckDir: KEGGgraph.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/KEGGgraph.Rcheck’
* using R version 2.13.2 (2011-09-30)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘KEGGgraph/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘KEGGgraph’ version ‘1.8.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... 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 examples ... OK
* checking for unstated dependencies in tests ... NOTE
'library' or 'require' call not declared from: RUnit
* checking tests ...
  Running ‘kegg2graph.R’
  Running ‘testGraph.R’
 OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: RColorBrewer
* 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

* installing *source* package ‘KEGGgraph’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (KEGGgraph)

name	user	system	elapsed
KEGGEdge-class	1.084	0.020	1.106
KEGGEdgeSubType-class	0.000	0.000	0.001
KEGGEdgeSubtype	0.012	0.000	0.009
KEGGGraphics-class	0.000	0.000	0.001
KEGGGroup-class	0.000	0.000	0.001
KEGGNode-class	0.672	0.004	0.679
KEGGPathway-class	1.064	0.000	1.064
KEGGPathwayInfo-class	0.708	0.000	0.711
KEGGReaction-class	1.088	0.004	1.092
KEGGpathway2Graph	0.740	0.008	0.748
KEGGpathway2reactionGraph	1.188	0.008	1.276
expandKEGGPathway	1.724	0.000	1.824
getDisplayName-methods	0.772	0.008	0.832
getEntryID-methods	0.900	0.004	1.240
getKEGGID-methods	0.348	0.000	0.362
getKEGGgeneLink-methods	0.000	0.000	0.001
getKEGGnodeData	1.700	0.020	1.749
getKGMLurl	0.008	0.016	3.109
getName-methods	0.628	0.020	0.648
getNamedElement	0	0	0
getPathwayInfo-methods	0.548	0.004	0.555
getReactions-methods	0.988	0.000	0.989
getRgraphvizEdgeNames	0.004	0.000	0.003
getSubtype-methods	0.741	0.004	0.754
getTitle-methods	0.604	0.004	0.607
getType-methods	1.064	0.000	1.076
graphDensity	0.004	0.000	0.004
isHomoList	0.000	0.000	0.001
mergeKEGGgraphs	3.524	0.016	3.540
neighborhood	0.024	0.000	0.026
parseKGML	0.660	0.012	0.669
parseKGML2Graph	1.840	0.004	1.845
plotKEGGgraph	3.688	0.008	3.697
pvalue2asterisk	0.000	0.000	0.001
queryKEGGsubgraph	1.608	0.000	1.631
randomSubGraph	0.036	0.000	0.032
splitKEGGgroup	0.704	0.000	0.706
subGraphByNodeType	1.917	0.000	1.916
subKEGGgraph	1.796	0.004	1.799
translateKEGGID2GeneID	0	0	0
translateKEGGgraph	1.820	0.000	1.826