BioC 3.2: CHECK report for KEGGgraph on oaxaca

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: 2016-04-23 01:31:27 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 01:32:41 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 74.2 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_1.28.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/KEGGgraph.Rcheck’
* using R version 3.2.4 (2016-03-10)
* 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 ‘1.28.0’
* 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 ... [22s/22s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘kegg2graph.R’ [10s/12s]
  Running ‘testGraph.R’ [2s/2s]
 [12s/14s] 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	0.588	0.005	0.593
KEGGEdgeSubType-class	0.002	0.000	0.001
KEGGEdgeSubtype	0.008	0.002	0.009
KEGGGraphics-class	0.001	0.000	0.001
KEGGGroup-class	0.001	0.001	0.002
KEGGNode-class	0.407	0.002	0.410
KEGGPathway-class	0.641	0.008	0.650
KEGGPathwayInfo-class	0.377	0.001	0.378
KEGGReaction-class	0.558	0.003	0.561
KEGGpathway2Graph	0.423	0.006	0.429
KEGGpathway2reactionGraph	0.603	0.002	0.605
expandKEGGPathway	0.828	0.004	0.832
getDisplayName-methods	0.368	0.002	0.370
getEntryID-methods	0.340	0.001	0.340
getKEGGID-methods	0.177	0.001	0.178
getKEGGgeneLink-methods	0	0	0
getKEGGnodeData	0.936	0.005	0.949
getKGMLurl	0.005	0.002	0.114
getName-methods	0.352	0.002	0.353
getNamedElement	0.000	0.000	0.001
getPathwayInfo-methods	0.364	0.001	0.365
getReactions-methods	0.674	0.002	0.680
getRgraphvizEdgeNames	0.002	0.000	0.002
getSubtype-methods	0.355	0.001	0.356
getTitle-methods	0.428	0.002	0.430
getType-methods	0.669	0.002	0.673
graphDensity	0.003	0.001	0.003
isHomoList	0.001	0.000	0.001
mergeKEGGgraphs	1.565	0.011	1.585
neighborhood	0.186	0.007	0.332
parseKGML	0.332	0.006	0.339
parseKGML2DataFrame	2.070	0.007	2.084
parseKGML2Graph	0.981	0.003	0.989
plotKEGGgraph	1.779	0.008	1.816
pvalue2asterisk	0.001	0.000	0.001
queryKEGGsubgraph	1.017	0.007	1.025
randomSubGraph	0.021	0.000	0.022
splitKEGGgroup	0.345	0.001	0.346
subGraphByNodeType	0.865	0.004	0.873
subKEGGgraph	0.972	0.003	0.977
translateKEGGID2GeneID	0.001	0.000	0.001
translateKEGGgraph	1.007	0.006	1.015