BioC 3.0: CHECK report for KEGGgraph on moscato1

Package: KEGGgraph

Version: 1.24.0

Command: rm -rf KEGGgraph.buildbin-libdir KEGGgraph.Rcheck && mkdir KEGGgraph.buildbin-libdir KEGGgraph.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=KEGGgraph.buildbin-libdir KEGGgraph_1.24.0.tar.gz >KEGGgraph.Rcheck\00install.out 2>&1 && cp KEGGgraph.Rcheck\00install.out KEGGgraph-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=KEGGgraph.buildbin-libdir --install="check:KEGGgraph-install.out" --force-multiarch --no-vignettes --timings KEGGgraph_1.24.0.tar.gz

StartedAt: 2015-04-10 02:31:09 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 02:33:36 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 146.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: KEGGgraph.Rcheck

Warnings: 1

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### Running command:
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###   rm -rf KEGGgraph.buildbin-libdir KEGGgraph.Rcheck && mkdir KEGGgraph.buildbin-libdir KEGGgraph.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=KEGGgraph.buildbin-libdir KEGGgraph_1.24.0.tar.gz >KEGGgraph.Rcheck\00install.out 2>&1 && cp KEGGgraph.Rcheck\00install.out KEGGgraph-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=KEGGgraph.buildbin-libdir --install="check:KEGGgraph-install.out" --force-multiarch --no-vignettes --timings KEGGgraph_1.24.0.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/KEGGgraph.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* 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 whether package 'KEGGgraph' can be installed ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... [25s] OK
** running examples for arch 'x64' ... [27s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'kegg2graph.R' [11s]
  Running 'testGraph.R' [1s]
 [13s] OK
** running tests for arch 'x64' ...
  Running 'kegg2graph.R' [12s]
  Running 'testGraph.R' [2s]
 [15s] 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
  'D:/biocbld/bbs-3.0-bioc/meat/KEGGgraph.Rcheck/00check.log'
for details.

install for i386

* 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

install for x64

* installing *source* package 'KEGGgraph' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'KEGGgraph' as KEGGgraph_1.24.0.zip
* DONE (KEGGgraph)

name	user	system	elapsed
KEGGEdge-class	0.59	0.00	0.59
KEGGEdgeSubType-class	0	0	0
KEGGEdgeSubtype	0.02	0.00	0.02
KEGGGraphics-class	0	0	0
KEGGGroup-class	0	0	0
KEGGNode-class	0.33	0.00	0.33
KEGGPathway-class	0.56	0.00	0.56
KEGGPathwayInfo-class	0.31	0.00	0.31
KEGGReaction-class	0.53	0.01	0.55
KEGGpathway2Graph	0.41	0.00	0.40
KEGGpathway2reactionGraph	0.64	0.00	0.64
expandKEGGPathway	0.71	0.00	0.72
getDisplayName-methods	0.32	0.00	0.31
getEntryID-methods	0.36	0.00	0.36
getKEGGID-methods	0.17	0.00	0.17
getKEGGgeneLink-methods	0	0	0
getKEGGnodeData	0.91	0.00	0.90
getKGMLurl	0.01	0.00	1.42
getName-methods	0.32	0.02	0.33
getNamedElement	0	0	0
getPathwayInfo-methods	0.32	0.02	0.34
getReactions-methods	0.56	0.00	0.56
getRgraphvizEdgeNames	0	0	0
getSubtype-methods	0.35	0.00	0.35
getTitle-methods	0.33	0.00	0.32
getType-methods	0.65	0.00	0.66
graphDensity	0	0	0
isHomoList	0	0	0
mergeKEGGgraphs	2.06	0.00	2.06
neighborhood	0.2	0.0	0.2
parseKGML	0.35	0.00	0.35
parseKGML2DataFrame	2.16	0.00	2.16
parseKGML2Graph	0.99	0.00	0.99
plotKEGGgraph	2.54	0.00	2.54
pvalue2asterisk	0	0	0
queryKEGGsubgraph	1.45	0.01	1.47
randomSubGraph	0.03	0.00	0.03
splitKEGGgroup	0.48	0.00	0.49
subGraphByNodeType	1.09	0.00	1.09
subKEGGgraph	1.46	0.00	1.47
translateKEGGID2GeneID	0	0	0
translateKEGGgraph	0.99	0.00	0.98

name	user	system	elapsed
KEGGEdge-class	0.72	0.00	0.72
KEGGEdgeSubType-class	0	0	0
KEGGEdgeSubtype	0.01	0.00	0.01
KEGGGraphics-class	0	0	0
KEGGGroup-class	0	0	0
KEGGNode-class	0.41	0.00	0.41
KEGGPathway-class	0.7	0.0	0.7
KEGGPathwayInfo-class	0.39	0.00	0.39
KEGGReaction-class	0.64	0.00	0.64
KEGGpathway2Graph	0.45	0.00	0.45
KEGGpathway2reactionGraph	0.77	0.02	0.78
expandKEGGPathway	0.85	0.00	0.86
getDisplayName-methods	0.37	0.00	0.37
getEntryID-methods	0.37	0.00	0.37
getKEGGID-methods	0.19	0.00	0.18
getKEGGgeneLink-methods	0	0	0
getKEGGnodeData	1.11	0.00	1.11
getKGMLurl	0.01	0.00	0.78
getName-methods	0.41	0.00	0.40
getNamedElement	0	0	0
getPathwayInfo-methods	0.39	0.01	0.41
getReactions-methods	0.72	0.00	0.72
getRgraphvizEdgeNames	0	0	0
getSubtype-methods	0.44	0.00	0.44
getTitle-methods	0.42	0.00	0.42
getType-methods	0.72	0.00	0.72
graphDensity	0.01	0.00	0.01
isHomoList	0	0	0
mergeKEGGgraphs	2.13	0.00	2.12
neighborhood	0.21	0.00	0.22
parseKGML	0.42	0.00	0.42
parseKGML2DataFrame	2.70	0.02	2.71
parseKGML2Graph	1.19	0.00	1.19
plotKEGGgraph	2.38	0.01	2.40
pvalue2asterisk	0	0	0
queryKEGGsubgraph	1.27	0.00	1.27
randomSubGraph	0.03	0.00	0.03
splitKEGGgroup	0.61	0.00	0.61
subGraphByNodeType	1.16	0.00	1.15
subKEGGgraph	1.20	0.00	1.21
translateKEGGID2GeneID	0	0	0
translateKEGGgraph	1.3	0.0	1.3