BioC 3.5: CHECK report for KEGGgraph on tokay2

Package: KEGGgraph

Version: 1.38.1

Command: rm -rf KEGGgraph.buildbin-libdir KEGGgraph.Rcheck && mkdir KEGGgraph.buildbin-libdir KEGGgraph.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=KEGGgraph.buildbin-libdir KEGGgraph_1.38.1.tar.gz >KEGGgraph.Rcheck\00install.out 2>&1 && cp KEGGgraph.Rcheck\00install.out KEGGgraph-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=KEGGgraph.buildbin-libdir --install="check:KEGGgraph-install.out" --force-multiarch --no-vignettes --timings KEGGgraph_1.38.1.tar.gz

StartedAt: 2017-08-16 00:47:15 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 00:49:09 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 113.7 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-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=KEGGgraph.buildbin-libdir KEGGgraph_1.38.1.tar.gz >KEGGgraph.Rcheck\00install.out 2>&1 && cp KEGGgraph.Rcheck\00install.out KEGGgraph-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=KEGGgraph.buildbin-libdir --install="check:KEGGgraph-install.out" --force-multiarch --no-vignettes --timings KEGGgraph_1.38.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/KEGGgraph.Rcheck'
* using R version 3.4.1 (2017-06-30)
* 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 '1.38.1'
* 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 ... OK
* 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'
Undefined global functions or variables:
  KEGGEdgeSubtype KEGGPATHID2NAME layoutGraph renderGraph
* 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' ... 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, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.5-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_1.38.1.zip
* DONE (KEGGgraph)

name	user	system	elapsed
KEGGEdge-class	0.36	0.00	0.36
KEGGEdgeSubType-class	0	0	0
KEGGEdgeSubtype	0.03	0.00	0.03
KEGGGraphics-class	0.02	0.00	0.01
KEGGGroup-class	0	0	0
KEGGNode-class	0.25	0.00	0.25
KEGGPathway-class	0.26	0.00	0.27
KEGGPathwayInfo-class	0.17	0.00	0.17
KEGGReaction-class	0.3	0.0	0.3
KEGGpathway2Graph	0.23	0.00	0.23
KEGGpathway2reactionGraph	0.40	0.02	0.41
expandKEGGPathway	0.42	0.00	0.42
getDisplayName-methods	0.17	0.00	0.17
getEntryID-methods	0.16	0.00	0.16
getKEGGID-methods	0.09	0.00	0.09
getKEGGgeneLink-methods	0	0	0
getKEGGnodeData	0.94	0.00	0.94
getKGMLurl	0.03	0.00	0.03
getName-methods	0.26	0.00	0.27
getNamedElement	0	0	0
getPathwayInfo-methods	0.25	0.01	0.26
getReactions-methods	0.46	0.02	0.47
getRgraphvizEdgeNames	0	0	0
getSubtype-methods	0.29	0.00	0.30
getTitle-methods	0.28	0.00	0.28
getType-methods	0.47	0.00	0.47
graphDensity	0	0	0
isHomoList	0.02	0.00	0.01
mergeKEGGgraphs	1.55	0.01	1.57
neighborhood	0.17	0.00	0.17
parseKGML	0.18	0.00	0.18
parseKGML2DataFrame	1.9	0.0	1.9
parseKGML2Graph	0.47	0.00	0.47
plotKEGGgraph	1.17	0.00	1.17
pvalue2asterisk	0.02	0.00	0.02
queryKEGGsubgraph	0.58	0.00	0.58
randomSubGraph	0.01	0.00	0.01
splitKEGGgroup	0.16	0.00	0.16
subGraphByNodeType	0.54	0.02	0.56
subKEGGgraph	0.58	0.00	0.58
translateKEGGID2GeneID	0	0	0
translateKEGGgraph	0.60	0.00	0.59

name	user	system	elapsed
KEGGEdge-class	0.60	0.00	0.59
KEGGEdgeSubType-class	0	0	0
KEGGEdgeSubtype	0.03	0.00	0.03
KEGGGraphics-class	0	0	0
KEGGGroup-class	0	0	0
KEGGNode-class	0.39	0.01	0.40
KEGGPathway-class	0.35	0.00	0.35
KEGGPathwayInfo-class	0.2	0.0	0.2
KEGGReaction-class	0.33	0.00	0.33
KEGGpathway2Graph	0.28	0.00	0.28
KEGGpathway2reactionGraph	0.5	0.0	0.5
expandKEGGPathway	0.8	0.0	0.8
getDisplayName-methods	0.32	0.00	0.33
getEntryID-methods	0.32	0.02	0.32
getKEGGID-methods	0.11	0.00	0.11
getKEGGgeneLink-methods	0.01	0.00	0.02
getKEGGnodeData	0.86	0.00	0.86
getKGMLurl	0.02	0.00	0.01
getName-methods	0.22	0.00	0.22
getNamedElement	0	0	0
getPathwayInfo-methods	0.23	0.00	0.24
getReactions-methods	0.41	0.01	0.42
getRgraphvizEdgeNames	0	0	0
getSubtype-methods	0.23	0.00	0.23
getTitle-methods	0.25	0.00	0.25
getType-methods	0.38	0.00	0.38
graphDensity	0	0	0
isHomoList	0	0	0
mergeKEGGgraphs	1.53	0.00	1.53
neighborhood	0.2	0.0	0.2
parseKGML	0.28	0.00	0.28
parseKGML2DataFrame	1.73	0.02	1.75
parseKGML2Graph	0.58	0.00	0.58
plotKEGGgraph	1.51	0.00	1.51
pvalue2asterisk	0.02	0.00	0.02
queryKEGGsubgraph	0.69	0.00	0.69
randomSubGraph	0.01	0.00	0.01
splitKEGGgroup	0.25	0.00	0.25
subGraphByNodeType	0.71	0.00	0.70
subKEGGgraph	0.78	0.00	0.79
translateKEGGID2GeneID	0	0	0
translateKEGGgraph	0.69	0.00	0.68