BioC 3.1: CHECK report for KEGGgraph on zin2

Package: KEGGgraph

Version: 1.26.0

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings KEGGgraph_1.26.0.tar.gz

StartedAt: 2015-10-09 02:54:23 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 02:55:48 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 85.0 seconds

RetCode: 0

Status:  OK

CheckDir: KEGGgraph.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings KEGGgraph_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/KEGGgraph.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-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 ‘1.26.0’
* 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 ... [2s/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<-’
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 ... [17s/25s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘kegg2graph.R’ [7s/11s]
  Running ‘testGraph.R’ [1s/2s]
 [9s/13s] 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
  ‘/home/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	0.446	0.000	0.630
KEGGEdgeSubType-class	0.001	0.000	0.001
KEGGEdgeSubtype	0.008	0.000	0.016
KEGGGraphics-class	0.001	0.000	0.001
KEGGGroup-class	0.001	0.000	0.004
KEGGNode-class	0.273	0.000	0.455
KEGGPathway-class	0.485	0.004	0.808
KEGGPathwayInfo-class	0.248	0.000	0.280
KEGGReaction-class	0.412	0.000	0.412
KEGGpathway2Graph	0.296	0.004	0.300
KEGGpathway2reactionGraph	0.472	0.001	0.707
expandKEGGPathway	0.559	0.008	0.831
getDisplayName-methods	0.26	0.00	0.26
getEntryID-methods	0.264	0.000	0.520
getKEGGID-methods	0.146	0.000	0.278
getKEGGgeneLink-methods	0.001	0.000	0.001
getKEGGnodeData	0.762	0.004	1.234
getKGMLurl	0.002	0.008	0.945
getName-methods	0.265	0.012	0.309
getNamedElement	0.001	0.000	0.001
getPathwayInfo-methods	0.277	0.000	0.424
getReactions-methods	0.469	0.002	0.698
getRgraphvizEdgeNames	0.002	0.000	0.013
getSubtype-methods	0.272	0.007	0.299
getTitle-methods	0.280	0.000	0.294
getType-methods	0.478	0.000	0.682
graphDensity	0.002	0.000	0.002
isHomoList	0.001	0.000	0.001
mergeKEGGgraphs	1.329	0.020	2.213
neighborhood	0.131	0.004	0.172
parseKGML	0.266	0.000	0.358
parseKGML2DataFrame	1.772	0.000	2.837
parseKGML2Graph	0.837	0.011	1.231
plotKEGGgraph	1.286	0.004	2.010
pvalue2asterisk	0.001	0.000	0.001
queryKEGGsubgraph	0.729	0.000	0.890
randomSubGraph	0.013	0.000	0.032
splitKEGGgroup	0.267	0.000	0.294
subGraphByNodeType	0.722	0.000	1.005
subKEGGgraph	0.744	0.004	1.300
translateKEGGID2GeneID	0.001	0.000	0.001
translateKEGGgraph	0.765	0.000	1.036