BioC 3.4: CHECK report for KEGGgraph on moscato1

Package: KEGGgraph

Version: 1.31.0

Command: rm -rf KEGGgraph.buildbin-libdir KEGGgraph.Rcheck && mkdir KEGGgraph.buildbin-libdir KEGGgraph.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=KEGGgraph.buildbin-libdir KEGGgraph_1.31.0.tar.gz >KEGGgraph.Rcheck\00install.out 2>&1 && cp KEGGgraph.Rcheck\00install.out KEGGgraph-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=KEGGgraph.buildbin-libdir --install="check:KEGGgraph-install.out" --force-multiarch --no-vignettes --timings KEGGgraph_1.31.0.tar.gz

StartedAt: 2016-09-20 11:00:27 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 11:02:27 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 120.0 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-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=KEGGgraph.buildbin-libdir KEGGgraph_1.31.0.tar.gz >KEGGgraph.Rcheck\00install.out 2>&1 && cp KEGGgraph.Rcheck\00install.out KEGGgraph-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=KEGGgraph.buildbin-libdir --install="check:KEGGgraph-install.out" --force-multiarch --no-vignettes --timings KEGGgraph_1.31.0.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/KEGGgraph.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-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 '1.31.0'
* 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 ... OK
* 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 global function definition for 'data'
.subtypeDisplay: no visible binding for global variable
  'KEGGEdgeSubtype'
KEGGgraphLegend: no visible global function definition for 'par'
KEGGgraphLegend: no visible global function definition for 'data'
KEGGgraphLegend: no visible binding for global variable
  'KEGGEdgeSubtype'
KEGGgraphLegend: no visible global function definition for 'text'
KEGGgraphLegend: no visible global function definition for 'segments'
getCategoryIndepKGMLurl: no visible global function definition for
  'download.file'
kgmlFileName2PathwayName: no visible binding for global variable
  'KEGGPATHID2NAME'
parseKGMLexpandMaps: no visible global function definition for
  'download.file'
plotKEGGgraph: no visible global function definition for 'layoutGraph'
plotKEGGgraph: no visible global function definition for 'renderGraph'
retrieveKGML: no visible global function definition for 'download.file'
subtypeDisplay,graph: no visible binding for global variable 'test'
subtypeDisplay,graph: no visible binding for global variable
  'keggeEdgesDisplay'
Undefined global functions or variables:
  KEGGEdgeSubtype KEGGPATHID2NAME data download.file keggeEdgesDisplay
  layoutGraph par renderGraph segments test text
Consider adding
  importFrom("graphics", "par", "segments", "text")
  importFrom("utils", "data", "download.file")
to your NAMESPACE file.
* 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 ... WARNING
  Warning: package needs dependence on R (>= 2.10)
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'kegg2graph.R'
  Running 'testGraph.R'
 OK
** running tests for arch 'x64' ...
  Running 'kegg2graph.R'
  Running 'testGraph.R'
 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: 1 WARNING, 2 NOTEs
See
  'D:/biocbld/bbs-3.4-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_1.31.0.zip
* DONE (KEGGgraph)

name	user	system	elapsed
KEGGEdge-class	0.40	0.01	0.42
KEGGEdgeSubType-class	0.02	0.00	0.02
KEGGEdgeSubtype	0.00	0.02	0.01
KEGGGraphics-class	0	0	0
KEGGGroup-class	0	0	0
KEGGNode-class	0.22	0.00	0.22
KEGGPathway-class	0.42	0.00	0.43
KEGGPathwayInfo-class	0.23	0.00	0.23
KEGGReaction-class	0.39	0.00	0.39
KEGGpathway2Graph	0.28	0.00	0.28
KEGGpathway2reactionGraph	0.44	0.00	0.44
expandKEGGPathway	0.5	0.0	0.5
getDisplayName-methods	0.23	0.00	0.23
getEntryID-methods	0.25	0.00	0.25
getKEGGID-methods	0.13	0.00	0.12
getKEGGgeneLink-methods	0	0	0
getKEGGnodeData	0.67	0.00	0.68
getKGMLurl	0.00	0.00	1.32
getName-methods	0.26	0.00	0.27
getNamedElement	0	0	0
getPathwayInfo-methods	0.25	0.00	0.25
getReactions-methods	0.52	0.00	0.52
getRgraphvizEdgeNames	0.01	0.00	0.01
getSubtype-methods	0.28	0.00	0.28
getTitle-methods	0.28	0.00	0.28
getType-methods	0.49	0.00	0.49
graphDensity	0	0	0
isHomoList	0	0	0
mergeKEGGgraphs	1.45	0.00	1.45
neighborhood	0.20	0.02	0.22
parseKGML	0.24	0.00	0.24
parseKGML2DataFrame	1.59	0.00	1.59
parseKGML2Graph	0.68	0.01	0.70
plotKEGGgraph	1.38	0.03	1.40
pvalue2asterisk	0	0	0
queryKEGGsubgraph	0.79	0.00	0.80
randomSubGraph	0.02	0.00	0.01
splitKEGGgroup	0.32	0.00	0.33
subGraphByNodeType	0.68	0.00	0.67
subKEGGgraph	0.67	0.00	0.67
translateKEGGID2GeneID	0	0	0
translateKEGGgraph	0.71	0.00	0.72

name	user	system	elapsed
KEGGEdge-class	0.56	0.00	0.57
KEGGEdgeSubType-class	0	0	0
KEGGEdgeSubtype	0.04	0.00	0.03
KEGGGraphics-class	0	0	0
KEGGGroup-class	0	0	0
KEGGNode-class	0.3	0.0	0.3
KEGGPathway-class	0.56	0.00	0.56
KEGGPathwayInfo-class	0.3	0.0	0.3
KEGGReaction-class	0.48	0.00	0.48
KEGGpathway2Graph	0.32	0.00	0.32
KEGGpathway2reactionGraph	0.55	0.00	0.55
expandKEGGPathway	0.64	0.00	0.64
getDisplayName-methods	0.29	0.00	0.30
getEntryID-methods	0.32	0.00	0.31
getKEGGID-methods	0.15	0.00	0.15
getKEGGgeneLink-methods	0	0	0
getKEGGnodeData	0.83	0.00	0.83
getKGMLurl	0.00	0.02	0.64
getName-methods	0.31	0.00	0.31
getNamedElement	0	0	0
getPathwayInfo-methods	0.30	0.00	0.29
getReactions-methods	0.51	0.00	0.52
getRgraphvizEdgeNames	0.02	0.00	0.01
getSubtype-methods	0.31	0.00	0.32
getTitle-methods	0.31	0.00	0.31
getType-methods	0.51	0.00	0.52
graphDensity	0	0	0
isHomoList	0	0	0
mergeKEGGgraphs	1.81	0.00	1.81
neighborhood	0.17	0.00	0.17
parseKGML	0.3	0.0	0.3
parseKGML2DataFrame	1.96	0.00	1.97
parseKGML2Graph	0.84	0.00	0.84
plotKEGGgraph	1.58	0.01	1.59
pvalue2asterisk	0	0	0
queryKEGGsubgraph	0.92	0.00	0.93
randomSubGraph	0.01	0.00	0.02
splitKEGGgroup	0.34	0.00	0.34
subGraphByNodeType	0.91	0.00	0.90
subKEGGgraph	0.90	0.00	0.91
translateKEGGID2GeneID	0	0	0
translateKEGGgraph	0.97	0.00	0.97