KEGGgraph 1.1.0
Jitao David Zhang
| Bioconductor Changelog | | Snapshot Date: 2009-10-20 11:27:33 -0700 (Tue, 20 Oct 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_4/madman/Rpacks/KEGGgraph | | Last Changed Rev: 40061 / Revision: 42512 | | Last Changed Date: 2009-06-10 07:58:30 -0700 (Wed, 10 Jun 2009) |
| wilson1 | Linux (openSUSE 11.1) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK |
| pitt | Mac OS X Tiger (10.4.11) / i386 | OK | OK | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | [ OK ] | OK |
* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.4-bioc/meat/KEGGgraph.Rcheck'
* using R version 2.9.2 Patched (2009-08-24 r49420)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'KEGGgraph/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'KEGGgraph' version '1.1.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'KEGGgraph' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking for unstated 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 files against version 2 parser ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking data for non-ASCII characters ... OK
* checking examples ... OK
* checking tests ...
Running ‘kegg2graph.R’
Running ‘testGraph.R’
OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK
* Installing *source* package ‘KEGGgraph’ ...
** R
** data
** inst
** preparing package for lazy loading
Attaching package: 'graph'
The following object(s) are masked from package:XML :
addNode
** help
*** installing help indices
>>> Building/Updating help pages for package 'KEGGgraph'
Formats: text html latex example
KEGGEdge-class text html latex example
KEGGEdgeSubType-class text html latex example
KEGGEdgeSubtype text html latex example
KEGGGraphics-class text html latex example
KEGGGroup-class text html latex example
KEGGNode-class text html latex example
KEGGPathway-class text html latex example
KEGGPathwayInfo-class text html latex example
KEGGReaction-class text html latex example
KEGGpathway2Graph text html latex example
KEGGpathway2reactionGraph text html latex example
expandKEGGNode text html latex
expandKEGGPathway text html latex example
getDisplayName-methods text html latex example
getEntryID-methods text html latex example
getKEGGID-methods text html latex example
getKEGGgeneLink-methods text html latex example
getKEGGnodeData text html latex example
getKGMLurl text html latex example
getName-methods text html latex example
getNamedElement text html latex example
getPathwayInfo-methods text html latex example
getReactions-methods text html latex example
getRgraphvizEdgeNames text html latex example
getSubtype-methods text html latex example
getTitle-methods text html latex example
getType-methods text html latex example
getValue-methods text html latex
graphDensity text html latex example
isHomoList text html latex example
kgmlFileName2PathwayName text html latex
mergeGraphs text html latex
mergeKEGGgraphs text html latex example
neighborhood text html latex example
parseEntry text html latex
parseGraphics text html latex
parseKGML text html latex example
parseKGML2Graph text html latex example
parseKGMLexpandMaps text html latex
parsePathwayInfo text html latex
parseReaction text html latex
parseRelation text html latex
parseSubType text html latex
plotKEGGgraph text html latex example
pvalue2asterisk text html latex example
queryKEGGsubgraph text html latex example
randomSubGraph text html latex example
splitKEGGgroup text html latex example
subGraphByNodeType text html latex example
subKEGGgraph text html latex example
subtypeDisplay-methods text html latex
top text html latex
translateKEGGID2GeneID text html latex example
translateKEGGgraph text html latex example
** building package indices ...
* DONE (KEGGgraph)