BioC 2.14: CHECK report for KEGGgraph on zin2

Package: KEGGgraph

Version: 1.22.1

Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings KEGGgraph_1.22.1.tar.gz

StartedAt: 2014-10-08 00:41:41 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 00:42:53 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 72.9 seconds

RetCode: 0

Status:  OK

CheckDir: KEGGgraph.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings KEGGgraph_1.22.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/KEGGgraph.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-linux-gnu (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 ... [3s/3s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [22s/23s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘kegg2graph.R’ [10s/10s]
  Running ‘testGraph.R’ [1s/1s]
 [12s/12s] 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
  ‘/home/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	0.564	0.004	0.566
KEGGEdgeSubType-class	0.000	0.000	0.001
KEGGEdgeSubtype	0.008	0.000	0.008
KEGGGraphics-class	0.000	0.000	0.001
KEGGGroup-class	0.004	0.000	0.001
KEGGNode-class	0.336	0.004	0.343
KEGGPathway-class	0.576	0.004	0.580
KEGGPathwayInfo-class	0.328	0.000	0.329
KEGGReaction-class	0.548	0.008	0.555
KEGGpathway2Graph	0.384	0.004	0.389
KEGGpathway2reactionGraph	0.632	0.000	0.633
expandKEGGPathway	0.732	0.004	0.736
getDisplayName-methods	0.308	0.000	0.308
getEntryID-methods	0.308	0.000	0.307
getKEGGID-methods	0.160	0.000	0.163
getKEGGgeneLink-methods	0.000	0.000	0.001
getKEGGnodeData	0.992	0.000	0.994
getKGMLurl	0.004	0.000	0.906
getName-methods	0.324	0.000	0.326
getNamedElement	0.000	0.000	0.001
getPathwayInfo-methods	0.324	0.000	0.322
getReactions-methods	0.548	0.000	0.550
getRgraphvizEdgeNames	0.004	0.000	0.003
getSubtype-methods	0.328	0.000	0.327
getTitle-methods	0.336	0.000	0.335
getType-methods	0.620	0.008	0.629
graphDensity	0.004	0.000	0.003
isHomoList	0.000	0.000	0.001
mergeKEGGgraphs	1.844	0.012	1.860
neighborhood	0.172	0.000	0.169
parseKGML	0.328	0.004	0.331
parseKGML2DataFrame	2.360	0.004	2.366
parseKGML2Graph	1.128	0.004	1.132
plotKEGGgraph	2.021	0.000	2.039
pvalue2asterisk	0.000	0.000	0.001
queryKEGGsubgraph	1.000	0.004	1.006
randomSubGraph	0.020	0.000	0.018
splitKEGGgroup	0.328	0.000	0.327
subGraphByNodeType	1.004	0.000	1.028
subKEGGgraph	1.056	0.000	1.061
translateKEGGID2GeneID	0.000	0.000	0.001
translateKEGGgraph	1.076	0.004	1.079