BioC 3.2: CHECK report for KEGGgraph on perceval

Package: KEGGgraph

Version: 1.27.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings KEGGgraph_1.27.2.tar.gz

StartedAt: 2015-08-24 02:06:06 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 02:07:31 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 85.2 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_1.27.2.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 (2015-08-14 r69078)
* 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 ‘1.27.2’
* 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 ... [5s/5s] 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 ... [24s/24s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘kegg2graph.R’ [11s/12s]
  Running ‘testGraph.R’ [2s/2s]
 [14s/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	0.598	0.011	0.608
KEGGEdgeSubType-class	0.001	0.000	0.002
KEGGEdgeSubtype	0.009	0.001	0.011
KEGGGraphics-class	0.001	0.000	0.002
KEGGGroup-class	0.002	0.000	0.002
KEGGNode-class	0.366	0.003	0.370
KEGGPathway-class	0.670	0.017	0.688
KEGGPathwayInfo-class	0.336	0.003	0.338
KEGGReaction-class	0.564	0.005	0.570
KEGGpathway2Graph	0.435	0.004	0.439
KEGGpathway2reactionGraph	0.663	0.005	0.669
expandKEGGPathway	0.772	0.004	0.776
getDisplayName-methods	0.371	0.003	0.374
getEntryID-methods	0.367	0.003	0.370
getKEGGID-methods	0.233	0.003	0.235
getKEGGgeneLink-methods	0.001	0.000	0.001
getKEGGnodeData	1.185	0.009	1.194
getKGMLurl	0.007	0.003	0.012
getName-methods	0.435	0.003	0.439
getNamedElement	0.001	0.000	0.001
getPathwayInfo-methods	0.474	0.003	0.477
getReactions-methods	0.772	0.004	0.777
getRgraphvizEdgeNames	0.004	0.000	0.003
getSubtype-methods	0.445	0.003	0.448
getTitle-methods	0.409	0.002	0.411
getType-methods	0.741	0.003	0.744
graphDensity	0.004	0.000	0.003
isHomoList	0.001	0.000	0.002
mergeKEGGgraphs	1.756	0.014	1.782
neighborhood	0.252	0.006	0.258
parseKGML	0.351	0.001	0.353
parseKGML2DataFrame	2.585	0.025	2.612
parseKGML2Graph	0.889	0.008	0.897
plotKEGGgraph	2.004	0.016	2.022
pvalue2asterisk	0.001	0.000	0.002
queryKEGGsubgraph	1.063	0.008	1.071
randomSubGraph	0.020	0.001	0.021
splitKEGGgroup	0.374	0.002	0.377
subGraphByNodeType	1.017	0.003	1.020
subKEGGgraph	1.040	0.004	1.047
translateKEGGID2GeneID	0.001	0.000	0.001
translateKEGGgraph	1.140	0.006	1.150