BioC 3.2: CHECK report for KEGGgraph on moscato1

Package: KEGGgraph

Version: 1.27.2

Command: rm -rf KEGGgraph.buildbin-libdir KEGGgraph.Rcheck && mkdir KEGGgraph.buildbin-libdir KEGGgraph.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=KEGGgraph.buildbin-libdir KEGGgraph_1.27.2.tar.gz >KEGGgraph.Rcheck\00install.out 2>&1 && cp KEGGgraph.Rcheck\00install.out KEGGgraph-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=KEGGgraph.buildbin-libdir --install="check:KEGGgraph-install.out" --force-multiarch --no-vignettes --timings KEGGgraph_1.27.2.tar.gz

StartedAt: 2015-08-20 06:17:56 -0700 (Thu, 20 Aug 2015)

EndedAt: 2015-08-20 06:20:30 -0700 (Thu, 20 Aug 2015)

EllapsedTime: 154.6 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-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=KEGGgraph.buildbin-libdir KEGGgraph_1.27.2.tar.gz >KEGGgraph.Rcheck\00install.out 2>&1 && cp KEGGgraph.Rcheck\00install.out KEGGgraph-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=KEGGgraph.buildbin-libdir --install="check:KEGGgraph-install.out" --force-multiarch --no-vignettes --timings KEGGgraph_1.27.2.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/KEGGgraph.Rcheck'
* using R version 3.2.2 (2015-08-14)
* 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 '1.27.2'
* 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 binding for global variable
  'KEGGEdgeSubtype'
KEGGgraphLegend: no visible binding for global variable
  'KEGGEdgeSubtype'
kgmlFileName2PathwayName: no visible binding for global variable
  'KEGGPATHID2NAME'
plotKEGGgraph: no visible global function definition for 'layoutGraph'
plotKEGGgraph: no visible global function definition for 'renderGraph'
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 ... 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' ... [25s] OK
** running examples for arch 'x64' ... [28s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'kegg2graph.R' [11s]
  Running 'testGraph.R' [2s]
 [13s] OK
** running tests for arch 'x64' ...
  Running 'kegg2graph.R' [14s]
  Running 'testGraph.R' [1s]
 [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

Status: 1 WARNING, 2 NOTEs
See
  'D:/biocbld/bbs-3.2-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_1.27.2.zip
* DONE (KEGGgraph)

name	user	system	elapsed
KEGGEdge-class	0.61	0.00	0.61
KEGGEdgeSubType-class	0	0	0
KEGGEdgeSubtype	0.00	0.01	0.02
KEGGGraphics-class	0.02	0.00	0.01
KEGGGroup-class	0	0	0
KEGGNode-class	0.40	0.00	0.41
KEGGPathway-class	0.88	0.00	0.87
KEGGPathwayInfo-class	0.40	0.00	0.41
KEGGReaction-class	0.49	0.00	0.48
KEGGpathway2Graph	0.39	0.00	0.39
KEGGpathway2reactionGraph	0.61	0.00	0.61
expandKEGGPathway	0.73	0.00	0.73
getDisplayName-methods	0.44	0.00	0.44
getEntryID-methods	0.43	0.00	0.44
getKEGGID-methods	0.22	0.00	0.22
getKEGGgeneLink-methods	0	0	0
getKEGGnodeData	1.06	0.00	1.06
getKGMLurl	0.02	0.00	1.09
getName-methods	0.48	0.00	0.48
getNamedElement	0	0	0
getPathwayInfo-methods	0.33	0.00	0.33
getReactions-methods	0.69	0.00	0.69
getRgraphvizEdgeNames	0	0	0
getSubtype-methods	0.34	0.00	0.34
getTitle-methods	0.48	0.00	0.48
getType-methods	0.85	0.00	0.85
graphDensity	0	0	0
isHomoList	0	0	0
mergeKEGGgraphs	2.21	0.00	2.21
neighborhood	0.25	0.00	0.25
parseKGML	0.53	0.00	0.53
parseKGML2DataFrame	2.87	0.00	2.87
parseKGML2Graph	1.26	0.00	1.27
plotKEGGgraph	1.80	0.00	1.79
pvalue2asterisk	0	0	0
queryKEGGsubgraph	0.97	0.00	0.97
randomSubGraph	0.03	0.00	0.03
splitKEGGgroup	0.31	0.00	0.31
subGraphByNodeType	0.81	0.00	0.81
subKEGGgraph	0.87	0.00	0.87
translateKEGGID2GeneID	0	0	0
translateKEGGgraph	1.24	0.00	1.24

name	user	system	elapsed
KEGGEdge-class	0.58	0.00	0.58
KEGGEdgeSubType-class	0	0	0
KEGGEdgeSubtype	0.00	0.00	0.09
KEGGGraphics-class	0	0	0
KEGGGroup-class	0	0	0
KEGGNode-class	0.42	0.00	0.42
KEGGPathway-class	0.70	0.00	0.71
KEGGPathwayInfo-class	0.41	0.00	0.40
KEGGReaction-class	0.61	0.00	0.61
KEGGpathway2Graph	0.51	0.00	0.51
KEGGpathway2reactionGraph	0.69	0.00	0.69
expandKEGGPathway	0.89	0.02	0.91
getDisplayName-methods	0.54	0.00	0.54
getEntryID-methods	0.44	0.00	0.44
getKEGGID-methods	0.22	0.01	0.23
getKEGGgeneLink-methods	0	0	0
getKEGGnodeData	1	0	1
getKGMLurl	0.01	0.00	1.02
getName-methods	0.41	0.00	0.40
getNamedElement	0	0	0
getPathwayInfo-methods	0.53	0.00	0.53
getReactions-methods	0.74	0.00	0.73
getRgraphvizEdgeNames	0	0	0
getSubtype-methods	0.41	0.00	0.40
getTitle-methods	0.40	0.00	0.41
getType-methods	0.80	0.00	0.79
graphDensity	0	0	0
isHomoList	0	0	0
mergeKEGGgraphs	1.78	0.02	1.80
neighborhood	0.2	0.0	0.2
parseKGML	0.48	0.00	0.48
parseKGML2DataFrame	2.98	0.00	2.98
parseKGML2Graph	1.35	0.00	1.34
plotKEGGgraph	2.18	0.00	2.18
pvalue2asterisk	0	0	0
queryKEGGsubgraph	1.25	0.03	1.28
randomSubGraph	0.01	0.00	0.02
splitKEGGgroup	0.44	0.00	0.44
subGraphByNodeType	1.34	0.02	1.35
subKEGGgraph	1.13	0.00	1.13
translateKEGGID2GeneID	0	0	0
translateKEGGgraph	1.34	0.01	1.35