BioC 3.5: CHECK report for KEGGgraph on toluca2

Package: KEGGgraph

Version: 1.33.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings KEGGgraph_1.33.0.tar.gz

StartedAt: 2017-04-23 05:47:50 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 05:49:04 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 73.6 seconds

RetCode: 0

Status:  OK

CheckDir: KEGGgraph.Rcheck

Warnings: 0

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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_1.33.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/KEGGgraph.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.33.0’
* 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 ... 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 global function definition for ‘data’
.subtypeDisplay: no visible binding for global variable
  ‘KEGGEdgeSubtype’
KEGGgraphLegend: no visible global function definition for ‘par’
KEGGgraphLegend: no visible global function definition for ‘data’
KEGGgraphLegend: no visible binding for global variable
  ‘KEGGEdgeSubtype’
KEGGgraphLegend: no visible global function definition for ‘text’
KEGGgraphLegend: no visible global function definition for ‘segments’
getCategoryIndepKGMLurl: no visible global function definition for
  ‘download.file’
kgmlFileName2PathwayName: no visible binding for global variable
  ‘KEGGPATHID2NAME’
parseKGMLexpandMaps: no visible global function definition for
  ‘download.file’
plotKEGGgraph: no visible global function definition for ‘layoutGraph’
plotKEGGgraph: no visible global function definition for ‘renderGraph’
retrieveKGML: no visible global function definition for ‘download.file’
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 data download.file keggeEdgesDisplay
  layoutGraph par renderGraph segments test text
Consider adding
  importFrom("graphics", "par", "segments", "text")
  importFrom("utils", "data", "download.file")
to your NAMESPACE file.
* 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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-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	0.616	0.011	0.636
KEGGEdgeSubType-class	0.002	0.000	0.002
KEGGEdgeSubtype	0.024	0.003	0.027
KEGGGraphics-class	0.001	0.000	0.001
KEGGGroup-class	0.002	0.000	0.001
KEGGNode-class	0.348	0.002	0.350
KEGGPathway-class	0.497	0.004	0.507
KEGGPathwayInfo-class	0.317	0.008	0.327
KEGGReaction-class	0.475	0.005	0.487
KEGGpathway2Graph	0.355	0.002	0.359
KEGGpathway2reactionGraph	0.599	0.004	0.611
expandKEGGPathway	0.620	0.002	0.623
getDisplayName-methods	0.291	0.007	0.304
getEntryID-methods	0.273	0.001	0.280
getKEGGID-methods	0.147	0.000	0.151
getKEGGgeneLink-methods	0.001	0.000	0.001
getKEGGnodeData	1.023	0.007	1.064
getKGMLurl	0.026	0.000	0.027
getName-methods	0.290	0.002	0.302
getNamedElement	0.000	0.000	0.001
getPathwayInfo-methods	0.258	0.001	0.259
getReactions-methods	0.536	0.004	0.541
getRgraphvizEdgeNames	0.002	0.001	0.002
getSubtype-methods	0.281	0.001	0.284
getTitle-methods	0.286	0.001	0.287
getType-methods	0.528	0.003	0.535
graphDensity	0.003	0.000	0.004
isHomoList	0.001	0.000	0.001
mergeKEGGgraphs	1.606	0.014	1.627
neighborhood	0.250	0.005	0.257
parseKGML	0.285	0.002	0.288
parseKGML2DataFrame	2.199	0.013	2.250
parseKGML2Graph	0.764	0.006	0.778
plotKEGGgraph	1.865	0.011	1.889
pvalue2asterisk	0.017	0.000	0.017
queryKEGGsubgraph	0.817	0.008	0.855
randomSubGraph	0.015	0.000	0.016
splitKEGGgroup	0.272	0.001	0.280
subGraphByNodeType	0.780	0.003	0.790
subKEGGgraph	0.801	0.007	0.815
translateKEGGID2GeneID	0.001	0.000	0.001
translateKEGGgraph	0.863	0.007	0.881