BioC 2.14: CHECK report for KEGGgraph on petty

Package: KEGGgraph

Version: 1.22.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch KEGGgraph_1.22.1.tar.gz

StartedAt: 2014-10-07 22:40:36 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 22:43:21 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 165.6 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 --no-multiarch KEGGgraph_1.22.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/KEGGgraph.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘1.22.1’
* 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 ... [7s/7s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’ ‘XML’ ‘graph’
A package should be listed in only one of these fields.
* 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’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [49s/49s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
parseKGML2DataFrame 5.263  0.015   5.314
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘kegg2graph.R’ [24s/24s]
  Running ‘testGraph.R’ [4s/4s]
 [28s/28s] 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.14-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	1.313	0.009	1.334
KEGGEdgeSubType-class	0.002	0.000	0.003
KEGGEdgeSubtype	0.016	0.002	0.018
KEGGGraphics-class	0.002	0.001	0.003
KEGGGroup-class	0.003	0.000	0.003
KEGGNode-class	0.735	0.004	0.746
KEGGPathway-class	1.313	0.010	1.336
KEGGPathwayInfo-class	0.702	0.004	0.706
KEGGReaction-class	1.125	0.005	1.136
KEGGpathway2Graph	0.833	0.007	0.842
KEGGpathway2reactionGraph	1.413	0.009	1.458
expandKEGGPathway	1.619	0.006	1.636
getDisplayName-methods	0.709	0.004	0.714
getEntryID-methods	0.704	0.004	0.709
getKEGGID-methods	0.377	0.002	0.381
getKEGGgeneLink-methods	0.001	0.000	0.002
getKEGGnodeData	2.121	0.009	2.141
getKGMLurl	0.007	0.002	0.042
getName-methods	0.700	0.003	0.705
getNamedElement	0.001	0.000	0.001
getPathwayInfo-methods	0.679	0.003	0.687
getReactions-methods	1.255	0.006	1.278
getRgraphvizEdgeNames	0.005	0.000	0.006
getSubtype-methods	0.746	0.004	0.790
getTitle-methods	0.768	0.004	0.827
getType-methods	1.361	0.007	1.462
graphDensity	0.005	0.001	0.006
isHomoList	0.002	0.000	0.002
mergeKEGGgraphs	4.014	0.018	4.066
neighborhood	0.446	0.009	0.464
parseKGML	0.763	0.005	0.805
parseKGML2DataFrame	5.263	0.015	5.314
parseKGML2Graph	2.331	0.010	2.356
plotKEGGgraph	4.444	0.015	4.488
pvalue2asterisk	0.001	0.000	0.002
queryKEGGsubgraph	2.259	0.008	2.272
randomSubGraph	0.045	0.001	0.046
splitKEGGgroup	0.758	0.004	0.768
subGraphByNodeType	2.151	0.005	2.159
subKEGGgraph	2.209	0.006	2.222
translateKEGGID2GeneID	0.002	0.000	0.002
translateKEGGgraph	2.417	0.008	2.441