BioC 3.1: CHECK report for KEGGgraph on petty

Package: KEGGgraph

Version: 1.26.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings KEGGgraph_1.26.0.tar.gz

StartedAt: 2015-10-08 23:54:52 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 23:56:40 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 108.7 seconds

RetCode: 0

Status:  OK

CheckDir: KEGGgraph.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings KEGGgraph_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/KEGGgraph.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.26.0’
* 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 ... [5s/6s] 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 ... NOTE
'library' or 'require' call to ‘KEGG.db’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* 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’
getKEGGnodeData: no visible global function definition for ‘nodeData’
graphDensity: no visible global function definition for ‘numEdges’
graphDensity: no visible global function definition for ‘numNodes’
KEGGgraphLegend: no visible binding for global variable
  ‘KEGGEdgeSubtype’
KEGGpathway2Graph: no visible global function definition for
  ‘nodeDataDefaults<-’
KEGGpathway2Graph: no visible global function definition for
  ‘edgeDataDefaults<-’
KEGGpathway2reactionGraph: no visible global function definition for
  ‘ftM2graphNEL’
KEGGpathway2reactionGraph: no visible global function definition for
  ‘nodeDataDefaults<-’
KEGGpathway2reactionGraph: no visible global function definition for
  ‘edgeDataDefaults<-’
kgmlFileName2PathwayName: no visible binding for global variable
  ‘KEGGPATHID2NAME’
mergeKEGGgraphs : <anonymous>: no visible global function definition
  for ‘nodeDataDefaults’
mergeKEGGgraphs : <anonymous>: no visible global function definition
  for ‘edgeDataDefaults’
mergeKEGGgraphs: no visible global function definition for
  ‘nodeDataDefaults<-’
mergeKEGGgraphs: no visible global function definition for
  ‘edgeDataDefaults<-’
plotKEGGgraph: no visible global function definition for
  ‘edgeRenderInfo<-’
plotKEGGgraph: no visible global function definition for
  ‘nodeRenderInfo<-’
plotKEGGgraph: no visible global function definition for ‘layoutGraph’
plotKEGGgraph: no visible global function definition for ‘renderGraph’
randomSubGraph : <anonymous>: no visible global function definition for
  ‘subGraph’
setKEGGedgeData: no visible global function definition for
  ‘edgeDataDefaults<-’
setKEGGnodeData: no visible global function definition for
  ‘nodeDataDefaults<-’
subGraphByNodeType: no visible global function definition for
  ‘subGraph’
subKEGGgraph: no visible global function definition for ‘subGraph’
subKEGGgraph: no visible global function definition for
  ‘nodeDataDefaults’
subKEGGgraph: no visible global function definition for
  ‘edgeDataDefaults’
subKEGGgraph: no visible global function definition for
  ‘nodeDataDefaults<-’
subKEGGgraph: no visible global function definition for
  ‘edgeDataDefaults<-’
subtypeDisplay,graph : .local: no visible binding for global variable
  ‘test’
subtypeDisplay,graph : .local: no visible binding for global variable
  ‘keggeEdgesDisplay’
* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [32s/32s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘kegg2graph.R’ [15s/15s]
  Running ‘testGraph.R’ [2s/2s]
 [17s/17s] 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
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-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	0.657	0.005	0.661
KEGGEdgeSubType-class	0.001	0.000	0.001
KEGGEdgeSubtype	0.013	0.002	0.014
KEGGGraphics-class	0.002	0.000	0.002
KEGGGroup-class	0.002	0.000	0.002
KEGGNode-class	0.489	0.002	0.491
KEGGPathway-class	1.038	0.015	1.055
KEGGPathwayInfo-class	0.375	0.003	0.377
KEGGReaction-class	0.679	0.003	0.682
KEGGpathway2Graph	0.457	0.003	0.461
KEGGpathway2reactionGraph	0.906	0.003	0.911
expandKEGGPathway	1.124	0.003	1.128
getDisplayName-methods	0.427	0.002	0.428
getEntryID-methods	0.413	0.002	0.413
getKEGGID-methods	0.317	0.001	0.319
getKEGGgeneLink-methods	0.001	0.000	0.001
getKEGGnodeData	1.427	0.006	1.434
getKGMLurl	0.006	0.002	0.079
getName-methods	0.585	0.002	0.588
getNamedElement	0.001	0.000	0.001
getPathwayInfo-methods	0.592	0.002	0.594
getReactions-methods	0.874	0.003	0.877
getRgraphvizEdgeNames	0.003	0.000	0.003
getSubtype-methods	0.548	0.002	0.551
getTitle-methods	0.593	0.002	0.597
getType-methods	0.897	0.004	0.901
graphDensity	0.003	0.000	0.003
isHomoList	0.002	0.000	0.002
mergeKEGGgraphs	2.550	0.011	2.568
neighborhood	0.346	0.005	0.353
parseKGML	0.489	0.002	0.491
parseKGML2DataFrame	3.245	0.016	3.263
parseKGML2Graph	1.406	0.007	1.414
plotKEGGgraph	2.547	0.014	2.563
pvalue2asterisk	0.002	0.000	0.002
queryKEGGsubgraph	1.548	0.006	1.559
randomSubGraph	0.026	0.001	0.026
splitKEGGgroup	0.480	0.002	0.482
subGraphByNodeType	1.300	0.005	1.307
subKEGGgraph	1.401	0.005	1.407
translateKEGGID2GeneID	0.002	0.000	0.002
translateKEGGgraph	1.504	0.005	1.510