BioC 2.13: CHECK report for KEGGgraph on zin1

Package: KEGGgraph

Version: 1.20.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings KEGGgraph_1.20.0.tar.gz

StartedAt: 2014-04-05 02:05:21 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 02:06:43 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 81.6 seconds

RetCode: 0

Status:  OK

CheckDir: KEGGgraph.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/KEGGgraph.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.20.0’
* 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 ... [3s/3s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’ ‘XML’ ‘graph’
A package should be listed in only one of these fields.
* 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 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘KEGGgraph.Rnw’, ‘KEGGgraphApp.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [25s/26s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘kegg2graph.R’ [12s/12s]
  Running ‘testGraph.R’ [2s/2s]
 [14s/14s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-2.13-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	0.720	0.008	0.731
KEGGEdgeSubType-class	0.004	0.000	0.007
KEGGEdgeSubtype	0.012	0.000	0.011
KEGGGraphics-class	0.000	0.000	0.002
KEGGGroup-class	0.004	0.000	0.003
KEGGNode-class	0.356	0.004	0.361
KEGGPathway-class	0.692	0.008	0.700
KEGGPathwayInfo-class	0.332	0.000	0.333
KEGGReaction-class	0.568	0.000	0.568
KEGGpathway2Graph	0.424	0.000	0.427
KEGGpathway2reactionGraph	0.664	0.004	0.666
expandKEGGPathway	0.816	0.000	0.815
getDisplayName-methods	0.376	0.000	0.377
getEntryID-methods	0.460	0.000	0.462
getKEGGID-methods	0.172	0.004	0.173
getKEGGgeneLink-methods	0.000	0.000	0.003
getKEGGnodeData	1.004	0.004	1.009
getKGMLurl	0.008	0.000	1.246
getName-methods	0.372	0.004	0.375
getNamedElement	0.000	0.000	0.003
getPathwayInfo-methods	0.356	0.000	0.357
getReactions-methods	0.704	0.000	0.705
getRgraphvizEdgeNames	0.008	0.000	0.005
getSubtype-methods	0.320	0.000	0.322
getTitle-methods	0.328	0.000	0.327
getType-methods	0.576	0.000	0.575
graphDensity	0.004	0.004	0.009
isHomoList	0.004	0.000	0.004
mergeKEGGgraphs	1.952	0.000	1.956
neighborhood	0.280	0.004	0.283
parseKGML	0.336	0.000	0.335
parseKGML2DataFrame	2.508	0.004	2.517
parseKGML2Graph	1.065	0.004	1.069
plotKEGGgraph	2.336	0.004	2.345
pvalue2asterisk	0.000	0.004	0.005
queryKEGGsubgraph	1.116	0.004	1.120
randomSubGraph	0.032	0.000	0.031
splitKEGGgroup	0.452	0.004	0.457
subGraphByNodeType	1.128	0.004	1.134
subKEGGgraph	1.216	0.004	1.220
translateKEGGID2GeneID	0.004	0.000	0.005
translateKEGGgraph	1.252	0.000	1.256