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Package 218/419HostnameOS / ArchBUILDCHECKBUILD BIN
KEGGgraph 1.6.0
Jitao David Zhang
Snapshot Date: 2011-03-30 23:22:56 -0700 (Wed, 30 Mar 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_7/madman/Rpacks/KEGGgraph
Last Changed Rev: 50293 / Revision: 54281
Last Changed Date: 2010-10-17 22:34:23 -0700 (Sun, 17 Oct 2010)
lamb2 Linux (openSUSE 11.2) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: KEGGgraph
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Versions/2.12/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch KEGGgraph_1.6.0.tar.gz
StartedAt: 2011-03-31 06:25:35 -0700 (Thu, 31 Mar 2011)
EndedAt: 2011-03-31 06:27:49 -0700 (Thu, 31 Mar 2011)
EllapsedTime: 134.0 seconds
RetCode: 0
Status:  OK 
CheckDir: KEGGgraph.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.7-bioc/meat/KEGGgraph.Rcheck’
* using R version 2.12.2 Patched (2011-02-25 r54591)
* using platform: i386-apple-darwin9.8.0 (32-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 ‘1.6.0’
* 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 package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... 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 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 data for non-ASCII characters ... OK
* checking examples ... OK
* checking for unstated dependencies in tests ... NOTE
'library' or 'require' call not declared from: RUnit
* checking tests ...
  Running ‘kegg2graph.R’
  Running ‘testGraph.R’
 OK
* checking package vignettes in ‘inst/doc’ ... SKIPPED
* checking PDF version of manual ... OK

KEGGgraph.Rcheck/00install.out:

* 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

Loading required package: grid
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (KEGGgraph)

KEGGgraph.Rcheck/KEGGgraph-Ex.timings:

nameusersystemelapsed
KEGGEdge-class1.5720.0151.604
KEGGEdgeSubType-class0.0020.0010.001
KEGGEdgeSubtype0.0140.0020.016
KEGGGraphics-class0.0010.0000.001
KEGGGroup-class0.0020.0000.002
KEGGNode-class0.8430.0040.850
KEGGPathway-class1.4430.0141.468
KEGGPathwayInfo-class0.8890.0060.910
KEGGReaction-class1.5160.0091.547
KEGGpathway2Graph0.9930.0101.015
KEGGpathway2reactionGraph1.4820.0101.506
expandKEGGPathway2.0760.0092.111
getDisplayName-methods0.9400.0060.956
getEntryID-methods0.8320.0050.843
getKEGGID-methods0.4360.0030.442
getKEGGgeneLink-methods0.0000.0000.001
getKEGGnodeData2.4690.0142.514
getKGMLurl0.0080.0180.027
getName-methods0.8530.0210.884
getNamedElement0.0000.0010.000
getPathwayInfo-methods0.8810.0060.899
getReactions-methods1.5370.0111.578
getRgraphvizEdgeNames0.0040.0010.004
getSubtype-methods0.9210.0050.939
getTitle-methods0.9750.0120.999
getType-methods1.3890.0091.425
graphDensity0.0050.0010.005
isHomoList0.0020.0000.001
mergeKEGGgraphs4.5470.0244.625
neighborhood0.0350.0010.035
parseKGML0.8990.0050.925
parseKGML2Graph2.3340.0112.374
plotKEGGgraph5.0240.0335.123
pvalue2asterisk0.0000.0000.001
queryKEGGsubgraph2.5280.0102.554
randomSubGraph0.0480.0000.049
splitKEGGgroup0.8660.0050.871
subGraphByNodeType2.4440.0072.454
subKEGGgraph2.5790.0102.600
translateKEGGID2GeneID0.0010.0010.001
translateKEGGgraph2.4280.0062.439