BioC 2.13: CHECK report for KEGGgraph on perceval

Package: KEGGgraph

Version: 1.20.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch KEGGgraph_1.20.0.tar.gz

StartedAt: 2014-04-05 02:15:34 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 02:17:45 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 131.6 seconds

RetCode: 0

Status:  OK

CheckDir: KEGGgraph.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/KEGGgraph.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.20.0’
* 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 ... [6s/6s] 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘KEGGgraph.Rnw’, ‘KEGGgraphApp.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [38s/38s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘kegg2graph.R’ [19s/20s]
  Running ‘testGraph.R’ [3s/3s]
 [23s/23s] 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 3 notes.
See
  ‘/Users/biocbuild/bbs-2.13-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	1.085	0.016	1.108
KEGGEdgeSubType-class	0.015	0.001	0.016
KEGGEdgeSubtype	0.029	0.003	0.032
KEGGGraphics-class	0.005	0.001	0.005
KEGGGroup-class	0.005	0.000	0.006
KEGGNode-class	0.502	0.008	0.511
KEGGPathway-class	1.056	0.019	1.082
KEGGPathwayInfo-class	0.466	0.007	0.483
KEGGReaction-class	0.831	0.008	0.886
KEGGpathway2Graph	0.658	0.005	0.669
KEGGpathway2reactionGraph	1.010	0.007	1.020
expandKEGGPathway	1.090	0.008	1.103
getDisplayName-methods	0.536	0.004	0.545
getEntryID-methods	0.577	0.006	0.588
getKEGGID-methods	0.256	0.005	0.268
getKEGGgeneLink-methods	0.004	0.000	0.005
getKEGGnodeData	1.401	0.016	1.432
getKGMLurl	0.047	0.003	0.077
getName-methods	0.669	0.006	0.675
getNamedElement	0.009	0.000	0.010
getPathwayInfo-methods	0.670	0.004	0.675
getReactions-methods	1.134	0.009	1.152
getRgraphvizEdgeNames	0.012	0.000	0.013
getSubtype-methods	0.501	0.005	0.510
getTitle-methods	0.495	0.005	0.509
getType-methods	0.861	0.006	0.895
graphDensity	0.026	0.000	0.027
isHomoList	0.011	0.000	0.011
mergeKEGGgraphs	3.217	0.022	3.270
neighborhood	0.324	0.012	0.340
parseKGML	0.473	0.004	0.482
parseKGML2DataFrame	3.867	0.022	3.967
parseKGML2Graph	1.474	0.006	1.484
plotKEGGgraph	3.586	0.038	3.657
pvalue2asterisk	0.033	0.001	0.034
queryKEGGsubgraph	1.638	0.015	1.674
randomSubGraph	0.049	0.001	0.050
splitKEGGgroup	0.564	0.004	0.576
subGraphByNodeType	1.857	0.008	1.878
subKEGGgraph	1.686	0.006	1.707
translateKEGGID2GeneID	0.024	0.001	0.025
translateKEGGgraph	1.779	0.011	1.820