BioC 3.2: CHECK report for KEGGgraph on windows1.bioconductor.org

Package: KEGGgraph

Version: 1.28.0

Command: rm -rf KEGGgraph.buildbin-libdir KEGGgraph.Rcheck && mkdir KEGGgraph.buildbin-libdir KEGGgraph.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=KEGGgraph.buildbin-libdir KEGGgraph_1.28.0.tar.gz >KEGGgraph.Rcheck\00install.out 2>&1 && cp KEGGgraph.Rcheck\00install.out KEGGgraph-install.out && C:\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_1.28.0.tar.gz

StartedAt: 2015-10-27 02:59:43 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 03:01:12 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 89.2 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-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=KEGGgraph.buildbin-libdir KEGGgraph_1.28.0.tar.gz >KEGGgraph.Rcheck\00install.out 2>&1 && cp KEGGgraph.Rcheck\00install.out KEGGgraph-install.out  && C:\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_1.28.0.tar.gz
###
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* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/KEGGgraph.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* 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 '1.28.0'
* 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 : .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' ... [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]
 [8s] 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-3.2-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_1.28.0.zip
* DONE (KEGGgraph)

name	user	system	elapsed
KEGGEdge-class	0.34	0.00	0.34
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	0.42	0.00	0.43
KEGGPathwayInfo-class	0.2	0.0	0.2
KEGGReaction-class	0.33	0.00	0.33
KEGGpathway2Graph	0.23	0.00	0.23
KEGGpathway2reactionGraph	0.36	0.01	0.38
expandKEGGPathway	0.46	0.00	0.45
getDisplayName-methods	0.23	0.00	0.23
getEntryID-methods	0.20	0.00	0.21
getKEGGID-methods	0.13	0.00	0.12
getKEGGgeneLink-methods	0	0	0
getKEGGnodeData	0.59	0.00	0.60
getKGMLurl	0	0	0
getName-methods	0.22	0.00	0.21
getNamedElement	0	0	0
getPathwayInfo-methods	0.22	0.00	0.22
getReactions-methods	0.41	0.00	0.40
getRgraphvizEdgeNames	0	0	0
getSubtype-methods	0.31	0.00	0.31
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	1.01	0.02	1.03
neighborhood	0.11	0.01	0.12
parseKGML	0.23	0.00	0.23
parseKGML2DataFrame	1.36	0.02	1.38
parseKGML2Graph	0.75	0.03	0.78
plotKEGGgraph	1.19	0.00	1.18
pvalue2asterisk	0	0	0
queryKEGGsubgraph	0.75	0.00	0.75
randomSubGraph	0.01	0.00	0.01
splitKEGGgroup	0.20	0.00	0.21
subGraphByNodeType	0.58	0.00	0.58
subKEGGgraph	0.62	0.00	0.63
translateKEGGID2GeneID	0	0	0
translateKEGGgraph	0.73	0.00	0.74

name	user	system	elapsed
KEGGEdge-class	0.48	0.00	0.49
KEGGEdgeSubType-class	0	0	0
KEGGEdgeSubtype	0.02	0.00	0.01
KEGGGraphics-class	0	0	0
KEGGGroup-class	0	0	0
KEGGNode-class	0.28	0.00	0.28
KEGGPathway-class	0.52	0.00	0.52
KEGGPathwayInfo-class	0.26	0.00	0.26
KEGGReaction-class	0.42	0.00	0.43
KEGGpathway2Graph	0.32	0.00	0.31
KEGGpathway2reactionGraph	0.46	0.00	0.47
expandKEGGPathway	0.57	0.00	0.56
getDisplayName-methods	0.28	0.00	0.28
getEntryID-methods	0.28	0.00	0.28
getKEGGID-methods	0.16	0.00	0.16
getKEGGgeneLink-methods	0	0	0
getKEGGnodeData	0.76	0.00	0.76
getKGMLurl	0.02	0.00	0.02
getName-methods	0.28	0.00	0.28
getNamedElement	0	0	0
getPathwayInfo-methods	0.28	0.00	0.28
getReactions-methods	0.46	0.00	0.47
getRgraphvizEdgeNames	0.02	0.00	0.01
getSubtype-methods	0.3	0.0	0.3
getTitle-methods	0.29	0.00	0.30
getType-methods	0.52	0.00	0.51
graphDensity	0	0	0
isHomoList	0	0	0
mergeKEGGgraphs	1.41	0.00	1.40
neighborhood	0.17	0.00	0.17
parseKGML	0.32	0.00	0.32
parseKGML2DataFrame	2.18	0.02	2.20
parseKGML2Graph	0.67	0.03	0.70
plotKEGGgraph	1.49	0.00	1.49
pvalue2asterisk	0	0	0
queryKEGGsubgraph	0.86	0.00	0.86
randomSubGraph	0.03	0.00	0.03
splitKEGGgroup	0.28	0.00	0.28
subGraphByNodeType	0.72	0.00	0.72
subKEGGgraph	0.75	0.00	0.75
translateKEGGID2GeneID	0	0	0
translateKEGGgraph	1.12	0.00	1.12