BioC 3.3: CHECK report for KEGGgraph on windows2.bioconductor.org

Package: KEGGgraph

Version: 1.29.0

Command: rm -rf KEGGgraph.buildbin-libdir KEGGgraph.Rcheck && mkdir KEGGgraph.buildbin-libdir KEGGgraph.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=KEGGgraph.buildbin-libdir KEGGgraph_1.29.0.tar.gz >KEGGgraph.Rcheck\00install.out 2>&1 && cp KEGGgraph.Rcheck\00install.out KEGGgraph-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=KEGGgraph.buildbin-libdir --install="check:KEGGgraph-install.out" --force-multiarch --no-vignettes --timings KEGGgraph_1.29.0.tar.gz

StartedAt: 2015-10-27 03:30:51 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 03:32:21 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 89.7 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 && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=KEGGgraph.buildbin-libdir KEGGgraph_1.29.0.tar.gz >KEGGgraph.Rcheck\00install.out 2>&1 && cp KEGGgraph.Rcheck\00install.out KEGGgraph-install.out  && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=KEGGgraph.buildbin-libdir --install="check:KEGGgraph-install.out" --force-multiarch --no-vignettes --timings KEGGgraph_1.29.0.tar.gz
###
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* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/KEGGgraph.Rcheck'
* using R Under development (unstable) (2015-09-22 r69418)
* 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 '1.29.0'
* 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 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: no visible binding for global variable 'test'
subtypeDisplay,graph: no visible binding for global variable
  'keggeEdgesDisplay'
Undefined global functions or variables:
  KEGGEdgeSubtype KEGGPATHID2NAME keggeEdgesDisplay layoutGraph
  renderGraph test
* 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' ... [14s] OK
** running examples for arch 'x64' ... [18s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'kegg2graph.R' [7s]
  Running 'testGraph.R' [1s]
 [9s] OK
** running tests for arch 'x64' ...
  Running 'kegg2graph.R' [8s]
  Running 'testGraph.R' [1s]
 [10s] 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:/biocbld/bbs-3.3-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_1.29.0.zip
* DONE (KEGGgraph)

name	user	system	elapsed
KEGGEdge-class	0.44	0.00	0.43
KEGGEdgeSubType-class	0	0	0
KEGGEdgeSubtype	0.02	0.00	0.01
KEGGGraphics-class	0	0	0
KEGGGroup-class	0	0	0
KEGGNode-class	0.22	0.00	0.22
KEGGPathway-class	0.39	0.01	0.41
KEGGPathwayInfo-class	0.19	0.00	0.19
KEGGReaction-class	0.42	0.00	0.42
KEGGpathway2Graph	0.23	0.00	0.23
KEGGpathway2reactionGraph	0.36	0.00	0.36
expandKEGGPathway	0.41	0.00	0.41
getDisplayName-methods	0.22	0.00	0.22
getEntryID-methods	0.21	0.00	0.22
getKEGGID-methods	0.11	0.00	0.11
getKEGGgeneLink-methods	0	0	0
getKEGGnodeData	0.58	0.00	0.57
getKGMLurl	0	0	0
getName-methods	0.21	0.02	0.22
getNamedElement	0	0	0
getPathwayInfo-methods	0.20	0.00	0.21
getReactions-methods	0.36	0.00	0.36
getRgraphvizEdgeNames	0	0	0
getSubtype-methods	0.22	0.00	0.22
getTitle-methods	0.22	0.00	0.22
getType-methods	0.39	0.00	0.39
graphDensity	0	0	0
isHomoList	0	0	0
mergeKEGGgraphs	1.11	0.03	1.14
neighborhood	0.12	0.00	0.12
parseKGML	0.18	0.00	0.19
parseKGML2DataFrame	1.36	0.00	1.36
parseKGML2Graph	0.75	0.00	0.75
plotKEGGgraph	1.28	0.00	1.28
pvalue2asterisk	0	0	0
queryKEGGsubgraph	0.61	0.00	0.61
randomSubGraph	0.01	0.00	0.02
splitKEGGgroup	0.21	0.00	0.20
subGraphByNodeType	0.53	0.00	0.53
subKEGGgraph	0.55	0.00	0.55
translateKEGGID2GeneID	0	0	0
translateKEGGgraph	0.58	0.00	0.57

name	user	system	elapsed
KEGGEdge-class	0.41	0.00	0.41
KEGGEdgeSubType-class	0	0	0
KEGGEdgeSubtype	0.02	0.00	0.02
KEGGGraphics-class	0	0	0
KEGGGroup-class	0	0	0
KEGGNode-class	0.26	0.00	0.27
KEGGPathway-class	0.47	0.00	0.46
KEGGPathwayInfo-class	0.24	0.00	0.24
KEGGReaction-class	0.4	0.0	0.4
KEGGpathway2Graph	0.28	0.00	0.28
KEGGpathway2reactionGraph	0.48	0.02	0.50
expandKEGGPathway	0.54	0.00	0.53
getDisplayName-methods	0.26	0.00	0.27
getEntryID-methods	0.27	0.00	0.26
getKEGGID-methods	0.14	0.00	0.14
getKEGGgeneLink-methods	0	0	0
getKEGGnodeData	0.70	0.00	0.71
getKGMLurl	0.02	0.00	0.01
getName-methods	0.26	0.00	0.27
getNamedElement	0	0	0
getPathwayInfo-methods	0.33	0.00	0.33
getReactions-methods	0.45	0.00	0.45
getRgraphvizEdgeNames	0	0	0
getSubtype-methods	0.27	0.00	0.27
getTitle-methods	0.31	0.00	0.31
getType-methods	0.61	0.01	0.62
graphDensity	0	0	0
isHomoList	0.02	0.00	0.02
mergeKEGGgraphs	1.59	0.02	1.61
neighborhood	0.22	0.00	0.22
parseKGML	0.28	0.00	0.28
parseKGML2DataFrame	2.47	0.00	2.47
parseKGML2Graph	0.92	0.00	0.92
plotKEGGgraph	1.64	0.01	1.66
pvalue2asterisk	0	0	0
queryKEGGsubgraph	0.72	0.02	0.74
randomSubGraph	0.01	0.00	0.01
splitKEGGgroup	0.35	0.00	0.34
subGraphByNodeType	0.75	0.00	0.75
subKEGGgraph	0.75	0.00	0.75
translateKEGGID2GeneID	0	0	0
translateKEGGgraph	0.81	0.00	0.82