BioC 3.0: CHECK report for KEGGgraph on zin1

Package: KEGGgraph

Version: 1.24.0

Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings KEGGgraph_1.24.0.tar.gz

StartedAt: 2015-04-10 01:23:44 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 01:24:54 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 69.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: KEGGgraph.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings KEGGgraph_1.24.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/KEGGgraph.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.24.0’
* 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/4s] 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’
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<-’
getKEGGnodeData: no visible global function definition for ‘nodeData’
graphDensity: no visible global function definition for ‘numEdges’
graphDensity: no visible global function definition for ‘numNodes’
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<-’
* 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 ... WARNING
Found the following file(s) containing GNU extensions:
  Makefile
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif. See section ‘Writing portable packages’ in
the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [21s/23s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘kegg2graph.R’ [10s/10s]
  Running ‘testGraph.R’ [1s/2s]
 [11s/12s] 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

WARNING: There was 1 warning.
NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-3.0-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	0.540	0.004	0.564
KEGGEdgeSubType-class	0.000	0.000	0.001
KEGGEdgeSubtype	0.008	0.000	0.009
KEGGGraphics-class	0.000	0.000	0.001
KEGGGroup-class	0.004	0.000	0.001
KEGGNode-class	0.300	0.000	0.304
KEGGPathway-class	0.536	0.004	0.592
KEGGPathwayInfo-class	0.324	0.000	0.341
KEGGReaction-class	0.540	0.000	0.541
KEGGpathway2Graph	0.368	0.000	0.370
KEGGpathway2reactionGraph	0.608	0.008	0.617
expandKEGGPathway	0.668	0.000	0.670
getDisplayName-methods	0.304	0.004	0.367
getEntryID-methods	0.300	0.000	0.377
getKEGGID-methods	0.160	0.000	0.192
getKEGGgeneLink-methods	0.000	0.000	0.001
getKEGGnodeData	0.920	0.000	0.979
getKGMLurl	0.004	0.000	1.298
getName-methods	0.344	0.000	0.453
getNamedElement	0	0	0
getPathwayInfo-methods	0.336	0.004	0.340
getReactions-methods	0.556	0.004	0.623
getRgraphvizEdgeNames	0.004	0.000	0.002
getSubtype-methods	0.312	0.004	0.319
getTitle-methods	0.312	0.008	0.357
getType-methods	0.572	0.004	0.596
graphDensity	0.004	0.000	0.003
isHomoList	0.004	0.000	0.001
mergeKEGGgraphs	1.820	0.004	1.862
neighborhood	0.180	0.004	0.317
parseKGML	0.348	0.000	0.352
parseKGML2DataFrame	2.128	0.004	2.136
parseKGML2Graph	0.920	0.000	0.956
plotKEGGgraph	1.965	0.008	2.013
pvalue2asterisk	0.000	0.000	0.001
queryKEGGsubgraph	0.956	0.004	0.962
randomSubGraph	0.012	0.000	0.015
splitKEGGgroup	0.296	0.000	0.300
subGraphByNodeType	0.864	0.000	0.866
subKEGGgraph	0.880	0.000	0.896
translateKEGGID2GeneID	0.004	0.000	0.001
translateKEGGgraph	0.916	0.000	0.960