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: 2017-08-16 04:32:31 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 04:33:34 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 63.2 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 3.4.1 (2017-06-30)
* 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	0.465	0.006	0.479
KEGGEdgeSubType-class	0.001	0.000	0.001
KEGGEdgeSubtype	0.027	0.004	0.030
KEGGGraphics-class	0.001	0.000	0.001
KEGGGroup-class	0.002	0.001	0.002
KEGGNode-class	0.285	0.001	0.302
KEGGPathway-class	0.338	0.002	0.342
KEGGPathwayInfo-class	0.236	0.007	0.245
KEGGReaction-class	0.286	0.002	0.290
KEGGpathway2Graph	0.277	0.002	0.290
KEGGpathway2reactionGraph	0.404	0.002	0.417
expandKEGGPathway	0.485	0.003	0.492
getDisplayName-methods	0.187	0.001	0.192
getEntryID-methods	0.212	0.002	0.221
getKEGGID-methods	0.104	0.000	0.108
getKEGGgeneLink-methods	0.001	0.000	0.001
getKEGGnodeData	0.867	0.005	0.897
getKGMLurl	0.026	0.000	0.026
getName-methods	0.237	0.002	0.249
getNamedElement	0.000	0.000	0.001
getPathwayInfo-methods	0.236	0.001	0.243
getReactions-methods	0.388	0.002	0.401
getRgraphvizEdgeNames	0.002	0.000	0.003
getSubtype-methods	0.244	0.001	0.251
getTitle-methods	0.206	0.000	0.220
getType-methods	0.382	0.002	0.393
graphDensity	0.001	0.001	0.002
isHomoList	0.001	0.000	0.001
mergeKEGGgraphs	1.287	0.008	1.345
neighborhood	0.236	0.005	0.246
parseKGML	0.250	0.001	0.257
parseKGML2DataFrame	1.762	0.008	1.837
parseKGML2Graph	0.617	0.004	0.644
plotKEGGgraph	1.548	0.009	1.596
pvalue2asterisk	0.019	0.000	0.019
queryKEGGsubgraph	0.718	0.005	0.731
randomSubGraph	0.014	0.001	0.014
splitKEGGgroup	0.203	0.001	0.207
subGraphByNodeType	0.653	0.002	0.672
subKEGGgraph	0.660	0.001	0.694
translateKEGGID2GeneID	0	0	0
translateKEGGgraph	0.726	0.005	0.760