BioC 3.2: CHECK report for KEGGgraph on perceval

Package: KEGGgraph

Version: 1.28.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings KEGGgraph_1.28.0.tar.gz

StartedAt: 2015-10-27 09:16:04 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 09:17:23 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 78.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: KEGGgraph.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings KEGGgraph_1.28.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/KEGGgraph.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘KEGGgraph’ can be installed ... [4s/4s] 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
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [23s/23s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘kegg2graph.R’ [10s/10s]
  Running ‘testGraph.R’ [2s/2s]
 [12s/12s] 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
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/KEGGgraph.Rcheck/00check.log’
for details.

* 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
* DONE (KEGGgraph)

name	user	system	elapsed
KEGGEdge-class	0.600	0.005	0.605
KEGGEdgeSubType-class	0.001	0.000	0.001
KEGGEdgeSubtype	0.009	0.001	0.010
KEGGGraphics-class	0.001	0.000	0.002
KEGGGroup-class	0.002	0.000	0.002
KEGGNode-class	0.358	0.002	0.359
KEGGPathway-class	0.644	0.012	0.656
KEGGPathwayInfo-class	0.339	0.002	0.341
KEGGReaction-class	0.563	0.003	0.565
KEGGpathway2Graph	0.419	0.001	0.421
KEGGpathway2reactionGraph	0.637	0.002	0.638
expandKEGGPathway	0.763	0.002	0.765
getDisplayName-methods	0.371	0.001	0.373
getEntryID-methods	0.360	0.001	0.361
getKEGGID-methods	0.193	0.001	0.194
getKEGGgeneLink-methods	0	0	0
getKEGGnodeData	1.001	0.003	1.003
getKGMLurl	0.004	0.003	0.068
getName-methods	0.371	0.001	0.372
getNamedElement	0.001	0.000	0.001
getPathwayInfo-methods	0.380	0.001	0.381
getReactions-methods	0.626	0.002	0.628
getRgraphvizEdgeNames	0.003	0.001	0.003
getSubtype-methods	0.392	0.001	0.392
getTitle-methods	0.387	0.002	0.388
getType-methods	0.722	0.002	0.724
graphDensity	0.003	0.000	0.003
isHomoList	0.001	0.000	0.002
mergeKEGGgraphs	1.696	0.014	1.710
neighborhood	0.256	0.004	0.260
parseKGML	0.379	0.001	0.381
parseKGML2DataFrame	2.259	0.005	2.264
parseKGML2Graph	0.995	0.001	0.997
plotKEGGgraph	1.941	0.006	1.947
pvalue2asterisk	0.001	0.000	0.001
queryKEGGsubgraph	1.218	0.006	1.222
randomSubGraph	0.018	0.000	0.018
splitKEGGgroup	0.345	0.002	0.346
subGraphByNodeType	0.926	0.004	0.930
subKEGGgraph	0.958	0.003	0.962
translateKEGGID2GeneID	0.001	0.001	0.001
translateKEGGgraph	1.032	0.004	1.036