BioC 3.5: CHECK report for KEGGgraph on veracruz2

Package: KEGGgraph

Version: 1.38.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings KEGGgraph_1.38.1.tar.gz

StartedAt: 2017-10-18 05:16:51 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 05:17:49 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 58.0 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_1.38.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/KEGGgraph.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.38.1’
* 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 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 ... 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 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: 1 WARNING, 1 NOTE
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	0.497	0.010	0.529
KEGGEdgeSubType-class	0.001	0.000	0.001
KEGGEdgeSubtype	0.027	0.003	0.030
KEGGGraphics-class	0.001	0.000	0.001
KEGGGroup-class	0.002	0.000	0.001
KEGGNode-class	0.328	0.003	0.339
KEGGPathway-class	0.356	0.003	0.368
KEGGPathwayInfo-class	0.288	0.008	0.301
KEGGReaction-class	0.334	0.003	0.352
KEGGpathway2Graph	0.285	0.004	0.298
KEGGpathway2reactionGraph	0.384	0.004	0.397
expandKEGGPathway	0.497	0.003	0.514
getDisplayName-methods	0.223	0.002	0.230
getEntryID-methods	0.198	0.002	0.204
getKEGGID-methods	0.111	0.001	0.121
getKEGGgeneLink-methods	0.001	0.000	0.001
getKEGGnodeData	0.872	0.009	0.901
getKGMLurl	0.021	0.001	0.022
getName-methods	0.290	0.007	0.306
getNamedElement	0.001	0.000	0.001
getPathwayInfo-methods	0.198	0.001	0.204
getReactions-methods	0.331	0.003	0.340
getRgraphvizEdgeNames	0.001	0.000	0.003
getSubtype-methods	0.202	0.003	0.210
getTitle-methods	0.221	0.002	0.226
getType-methods	0.341	0.004	0.361
graphDensity	0.001	0.000	0.002
isHomoList	0.001	0.000	0.001
mergeKEGGgraphs	1.333	0.013	1.393
neighborhood	0.166	0.009	0.178
parseKGML	0.205	0.002	0.210
parseKGML2DataFrame	1.452	0.013	1.514
parseKGML2Graph	0.632	0.007	0.655
plotKEGGgraph	1.475	0.014	1.550
pvalue2asterisk	0.014	0.000	0.015
queryKEGGsubgraph	0.661	0.006	0.685
randomSubGraph	0.011	0.000	0.012
splitKEGGgroup	0.210	0.001	0.219
subGraphByNodeType	0.631	0.004	0.658
subKEGGgraph	0.664	0.006	0.698
translateKEGGID2GeneID	0.000	0.000	0.001
translateKEGGgraph	0.652	0.006	0.685