BioC 2.14: CHECK report for KEGGgraph on moscato2

Package: KEGGgraph

Version: 1.22.1

Command: rm -rf KEGGgraph.buildbin-libdir && mkdir KEGGgraph.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=KEGGgraph.buildbin-libdir KEGGgraph_1.22.1.tar.gz >KEGGgraph-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=KEGGgraph.buildbin-libdir --install="check:KEGGgraph-install.out" --force-multiarch --no-vignettes --timings KEGGgraph_1.22.1.tar.gz

StartedAt: 2014-10-08 02:24:23 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 02:26:45 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 141.5 seconds

RetCode: 0

Status:  OK

CheckDir: KEGGgraph.Rcheck

Warnings: 0

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### Running command:
###
###   rm -rf KEGGgraph.buildbin-libdir && mkdir KEGGgraph.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=KEGGgraph.buildbin-libdir KEGGgraph_1.22.1.tar.gz >KEGGgraph-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=KEGGgraph.buildbin-libdir --install="check:KEGGgraph-install.out" --force-multiarch --no-vignettes --timings KEGGgraph_1.22.1.tar.gz
###
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* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/KEGGgraph.Rcheck'
* using R version 3.1.1 (2014-07-10)
* using platform: i386-w64-mingw32 (32-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 '1.22.1'
* 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 ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'methods' 'XML' 'graph'
A package should be listed in only one of these fields.
* 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'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [24s] 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' [13s]
  Running 'testGraph.R' [2s]
 [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

NOTE: There were 2 notes.
See
  'E:/biocbld/bbs-2.14-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_1.22.1.zip
* DONE (KEGGgraph)

name	user	system	elapsed
KEGGEdge-class	0.6	0.0	0.6
KEGGEdgeSubType-class	0	0	0
KEGGEdgeSubtype	0	0	0
KEGGGraphics-class	0.02	0.00	0.02
KEGGGroup-class	0	0	0
KEGGNode-class	0.32	0.00	0.33
KEGGPathway-class	0.58	0.00	0.58
KEGGPathwayInfo-class	0.33	0.00	0.33
KEGGReaction-class	0.56	0.00	0.56
KEGGpathway2Graph	0.39	0.00	0.39
KEGGpathway2reactionGraph	0.64	0.02	0.66
expandKEGGPathway	0.78	0.00	0.78
getDisplayName-methods	0.34	0.00	0.34
getEntryID-methods	0.33	0.00	0.33
getKEGGID-methods	0.17	0.01	0.19
getKEGGgeneLink-methods	0	0	0
getKEGGnodeData	1.03	0.00	1.03
getKGMLurl	0.00	0.00	1.67
getName-methods	0.36	0.00	0.35
getNamedElement	0	0	0
getPathwayInfo-methods	0.35	0.00	0.35
getReactions-methods	0.59	0.00	0.59
getRgraphvizEdgeNames	0	0	0
getSubtype-methods	0.34	0.00	0.34
getTitle-methods	0.36	0.00	0.36
getType-methods	0.59	0.00	0.59
graphDensity	0	0	0
isHomoList	0	0	0
mergeKEGGgraphs	1.98	0.00	1.99
neighborhood	0.19	0.00	0.18
parseKGML	0.32	0.00	0.33
parseKGML2DataFrame	2.45	0.02	2.46
parseKGML2Graph	1.10	0.00	1.09
plotKEGGgraph	2.13	0.00	2.14
pvalue2asterisk	0	0	0
queryKEGGsubgraph	1.05	0.00	1.05
randomSubGraph	0.01	0.00	0.01
splitKEGGgroup	0.36	0.00	0.36
subGraphByNodeType	1.02	0.00	1.01
subKEGGgraph	1.04	0.00	1.04
translateKEGGID2GeneID	0	0	0
translateKEGGgraph	1.09	0.00	1.10

name	user	system	elapsed
KEGGEdge-class	0.72	0.00	0.72
KEGGEdgeSubType-class	0	0	0
KEGGEdgeSubtype	0.01	0.00	0.02
KEGGGraphics-class	0	0	0
KEGGGroup-class	0	0	0
KEGGNode-class	0.41	0.00	0.40
KEGGPathway-class	0.70	0.00	0.71
KEGGPathwayInfo-class	0.39	0.00	0.39
KEGGReaction-class	0.67	0.00	0.67
KEGGpathway2Graph	0.48	0.00	0.48
KEGGpathway2reactionGraph	0.8	0.0	0.8
expandKEGGPathway	0.94	0.00	0.93
getDisplayName-methods	0.40	0.00	0.41
getEntryID-methods	0.39	0.00	0.39
getKEGGID-methods	0.2	0.0	0.2
getKEGGgeneLink-methods	0	0	0
getKEGGnodeData	1.22	0.00	1.21
getKGMLurl	0.00	0.00	0.97
getName-methods	0.41	0.00	0.40
getNamedElement	0	0	0
getPathwayInfo-methods	0.42	0.00	0.42
getReactions-methods	0.7	0.0	0.7
getRgraphvizEdgeNames	0	0	0
getSubtype-methods	0.42	0.00	0.43
getTitle-methods	0.44	0.00	0.43
getType-methods	0.76	0.00	0.77
graphDensity	0	0	0
isHomoList	0	0	0
mergeKEGGgraphs	2.34	0.00	2.34
neighborhood	0.20	0.02	0.22
parseKGML	0.44	0.00	0.43
parseKGML2DataFrame	3.04	0.01	3.06
parseKGML2Graph	1.23	0.00	1.23
plotKEGGgraph	2.6	0.0	2.6
pvalue2asterisk	0	0	0
queryKEGGsubgraph	1.31	0.00	1.31
randomSubGraph	0.04	0.00	0.04
splitKEGGgroup	0.42	0.00	0.42
subGraphByNodeType	1.27	0.00	1.27
subKEGGgraph	1.35	0.00	1.35
translateKEGGID2GeneID	0	0	0
translateKEGGgraph	1.33	0.02	1.35