BioC 2.14: CHECK report for KEGGgraph on morelia

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 23:41:47 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 23:43:21 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 94.7 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-darwin13.1.0 (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 ... [4s/4s] 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 ... [27s/28s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘kegg2graph.R’ [13s/13s]
  Running ‘testGraph.R’ [2s/2s]
 [14s/15s] 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	0.764	0.006	0.770
KEGGEdgeSubType-class	0.001	0.001	0.001
KEGGEdgeSubtype	0.008	0.001	0.009
KEGGGraphics-class	0.001	0.000	0.001
KEGGGroup-class	0.001	0.000	0.002
KEGGNode-class	0.408	0.001	0.410
KEGGPathway-class	0.753	0.006	0.761
KEGGPathwayInfo-class	0.407	0.002	0.409
KEGGReaction-class	0.646	0.003	0.649
KEGGpathway2Graph	0.476	0.003	0.480
KEGGpathway2reactionGraph	0.790	0.006	0.797
expandKEGGPathway	0.896	0.004	0.900
getDisplayName-methods	0.435	0.003	0.439
getEntryID-methods	0.430	0.003	0.434
getKEGGID-methods	0.233	0.002	0.234
getKEGGgeneLink-methods	0.001	0.000	0.000
getKEGGnodeData	1.110	0.005	1.114
getKGMLurl	0.005	0.001	0.007
getName-methods	0.425	0.003	0.427
getNamedElement	0.001	0.000	0.001
getPathwayInfo-methods	0.407	0.002	0.409
getReactions-methods	0.707	0.003	0.711
getRgraphvizEdgeNames	0.003	0.000	0.003
getSubtype-methods	0.440	0.002	0.442
getTitle-methods	0.478	0.003	0.481
getType-methods	0.816	0.008	0.826
graphDensity	0.004	0.000	0.004
isHomoList	0.001	0.000	0.002
mergeKEGGgraphs	2.240	0.009	2.251
neighborhood	0.225	0.006	0.231
parseKGML	0.434	0.002	0.437
parseKGML2DataFrame	3.068	0.010	3.081
parseKGML2Graph	1.379	0.008	1.388
plotKEGGgraph	2.449	0.014	2.465
pvalue2asterisk	0.001	0.000	0.002
queryKEGGsubgraph	1.209	0.006	1.217
randomSubGraph	0.02	0.00	0.02
splitKEGGgroup	0.410	0.002	0.412
subGraphByNodeType	1.176	0.004	1.180
subKEGGgraph	1.282	0.005	1.288
translateKEGGID2GeneID	0.001	0.000	0.002
translateKEGGgraph	1.278	0.007	1.286