BioC 3.4: CHECK report for KEGGgraph on tokay1

Package: KEGGgraph

Version: 1.32.0

Command: rm -rf KEGGgraph.buildbin-libdir KEGGgraph.Rcheck && mkdir KEGGgraph.buildbin-libdir KEGGgraph.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=KEGGgraph.buildbin-libdir KEGGgraph_1.32.0.tar.gz >KEGGgraph.Rcheck\00install.out 2>&1 && cp KEGGgraph.Rcheck\00install.out KEGGgraph-install.out && C:\Users\biocbuild\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_1.32.0.tar.gz

StartedAt: 2017-04-14 23:11:27 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 23:12:59 -0400 (Fri, 14 Apr 2017)

EllapsedTime: 92.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: KEGGgraph.Rcheck

Warnings: 1

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### Running command:
###
###   rm -rf KEGGgraph.buildbin-libdir KEGGgraph.Rcheck && mkdir KEGGgraph.buildbin-libdir KEGGgraph.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=KEGGgraph.buildbin-libdir KEGGgraph_1.32.0.tar.gz >KEGGgraph.Rcheck\00install.out 2>&1 && cp KEGGgraph.Rcheck\00install.out KEGGgraph-install.out  && C:\Users\biocbuild\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_1.32.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/KEGGgraph.Rcheck'
* using R version 3.3.3 (2017-03-06)
* 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 '1.32.0'
* 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
  'C:/Users/biocbuild/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_1.32.0.zip
* DONE (KEGGgraph)

name	user	system	elapsed
KEGGEdge-class	0.36	0.00	0.36
KEGGEdgeSubType-class	0	0	0
KEGGEdgeSubtype	0.02	0.01	0.03
KEGGGraphics-class	0	0	0
KEGGGroup-class	0	0	0
KEGGNode-class	0.2	0.0	0.2
KEGGPathway-class	0.38	0.00	0.38
KEGGPathwayInfo-class	0.15	0.00	0.15
KEGGReaction-class	0.31	0.00	0.32
KEGGpathway2Graph	0.22	0.00	0.21
KEGGpathway2reactionGraph	0.36	0.00	0.36
expandKEGGPathway	0.39	0.00	0.39
getDisplayName-methods	0.19	0.00	0.19
getEntryID-methods	0.22	0.00	0.22
getKEGGID-methods	0.09	0.00	0.09
getKEGGgeneLink-methods	0	0	0
getKEGGnodeData	0.64	0.02	0.66
getKGMLurl	0.02	0.00	0.01
getName-methods	0.23	0.00	0.24
getNamedElement	0	0	0
getPathwayInfo-methods	0.30	0.00	0.29
getReactions-methods	0.36	0.00	0.36
getRgraphvizEdgeNames	0.01	0.00	0.02
getSubtype-methods	0.22	0.00	0.22
getTitle-methods	0.22	0.00	0.22
getType-methods	0.37	0.00	0.37
graphDensity	0	0	0
isHomoList	0	0	0
mergeKEGGgraphs	1.3	0.0	1.3
neighborhood	0.20	0.00	0.21
parseKGML	0.18	0.00	0.17
parseKGML2DataFrame	1.23	0.01	1.25
parseKGML2Graph	0.56	0.00	0.56
plotKEGGgraph	1.26	0.02	1.28
pvalue2asterisk	0	0	0
queryKEGGsubgraph	0.66	0.00	0.66
randomSubGraph	0.02	0.00	0.02
splitKEGGgroup	0.34	0.00	0.34
subGraphByNodeType	0.72	0.00	0.72
subKEGGgraph	0.58	0.00	0.58
translateKEGGID2GeneID	0	0	0
translateKEGGgraph	0.9	0.0	0.9

name	user	system	elapsed
KEGGEdge-class	0.69	0.00	0.68
KEGGEdgeSubType-class	0	0	0
KEGGEdgeSubtype	0.01	0.01	0.03
KEGGGraphics-class	0	0	0
KEGGGroup-class	0	0	0
KEGGNode-class	0.25	0.00	0.25
KEGGPathway-class	0.46	0.02	0.47
KEGGPathwayInfo-class	0.22	0.00	0.22
KEGGReaction-class	0.37	0.00	0.37
KEGGpathway2Graph	0.24	0.01	0.25
KEGGpathway2reactionGraph	0.42	0.02	0.44
expandKEGGPathway	0.47	0.00	0.47
getDisplayName-methods	0.25	0.01	0.26
getEntryID-methods	0.27	0.00	0.27
getKEGGID-methods	0.14	0.00	0.14
getKEGGgeneLink-methods	0	0	0
getKEGGnodeData	0.81	0.00	0.81
getKGMLurl	0	0	0
getName-methods	0.40	0.02	0.42
getNamedElement	0	0	0
getPathwayInfo-methods	0.27	0.00	0.27
getReactions-methods	0.44	0.00	0.44
getRgraphvizEdgeNames	0	0	0
getSubtype-methods	0.36	0.00	0.36
getTitle-methods	0.48	0.00	0.48
getType-methods	0.64	0.00	0.64
graphDensity	0.00	0.02	0.02
isHomoList	0	0	0
mergeKEGGgraphs	1.49	0.01	1.50
neighborhood	0.15	0.00	0.15
parseKGML	0.24	0.00	0.24
parseKGML2DataFrame	1.53	0.00	1.53
parseKGML2Graph	0.67	0.00	0.67
plotKEGGgraph	1.17	0.00	1.17
pvalue2asterisk	0	0	0
queryKEGGsubgraph	0.74	0.02	0.75
randomSubGraph	0.01	0.00	0.02
splitKEGGgroup	0.31	0.00	0.31
subGraphByNodeType	0.63	0.00	0.63
subKEGGgraph	0.64	0.00	0.64
translateKEGGID2GeneID	0	0	0
translateKEGGgraph	0.66	0.00	0.65