Package: KEGGgraph

Version: 1.15.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings KEGGgraph_1.15.0.tar.gz

StartedAt: 2013-03-25 02:40:22 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 02:42:56 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 154.4 seconds

RetCode: 0

Status:  OK

CheckDir: KEGGgraph.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/KEGGgraph.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* 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 ‘1.15.0’
* 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 ... [7s/7s] 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 ... [47s/49s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘kegg2graph.R’ [22s/22s]
  Running ‘testGraph.R’ [3s/3s]
 [25s/25s] 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
  ‘/home/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	1.380	0.040	1.835
KEGGEdgeSubType-class	0.016	0.000	0.017
KEGGEdgeSubtype	0.200	0.008	0.239
KEGGGraphics-class	0.024	0.000	0.023
KEGGGroup-class	0.012	0.004	0.015
KEGGNode-class	0.604	0.020	0.628
KEGGPathway-class	1.156	0.012	1.169
KEGGPathwayInfo-class	0.676	0.000	0.675
KEGGReaction-class	0.964	0.000	0.963
KEGGpathway2Graph	0.804	0.004	0.805
KEGGpathway2reactionGraph	1.180	0.004	1.184
expandKEGGPathway	1.668	0.004	1.674
getDisplayName-methods	0.888	0.008	0.899
getEntryID-methods	0.616	0.004	0.621
getKEGGID-methods	0.320	0.004	0.324
getKEGGgeneLink-methods	0.008	0.000	0.009
getKEGGnodeData	1.732	0.012	1.769
getKGMLurl	0.044	0.020	0.868
getName-methods	0.741	0.004	0.753
getNamedElement	0.012	0.000	0.014
getPathwayInfo-methods	0.744	0.000	0.747
getReactions-methods	1.092	0.004	1.097
getRgraphvizEdgeNames	0.020	0.000	0.017
getSubtype-methods	0.568	0.004	0.576
getTitle-methods	0.620	0.000	0.622
getType-methods	1.192	0.000	1.195
graphDensity	0.036	0.000	0.038
isHomoList	0.020	0.000	0.022
mergeKEGGgraphs	3.896	0.012	3.940
neighborhood	0.708	0.020	0.728
parseKGML	0.588	0.004	0.598
parseKGML2DataFrame	3.508	0.008	3.515
parseKGML2Graph	2.04	0.00	2.04
plotKEGGgraph	4.661	0.012	4.670
pvalue2asterisk	0.024	0.000	0.026
queryKEGGsubgraph	2.260	0.012	2.276
randomSubGraph	0.104	0.004	0.110
splitKEGGgroup	0.876	0.008	0.884
subGraphByNodeType	2.300	0.004	2.309
subKEGGgraph	1.984	0.016	2.000
translateKEGGID2GeneID	0.016	0.000	0.019
translateKEGGgraph	2.444	0.000	2.443