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Package 272/514HostnameOS / ArchBUILDCHECKBUILD BIN
KEGGgraph 1.10.0
Jitao David Zhang
Snapshot Date: 2012-03-23 18:21:46 -0700 (Fri, 23 Mar 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/KEGGgraph
Last Changed Rev: 59920 / Revision: 64395
Last Changed Date: 2011-10-31 15:59:03 -0700 (Mon, 31 Oct 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: KEGGgraph
Version: 1.10.0
Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings KEGGgraph_1.10.0.tar.gz
StartedAt: 2012-03-24 01:10:46 -0700 (Sat, 24 Mar 2012)
EndedAt: 2012-03-24 01:12:22 -0700 (Sat, 24 Mar 2012)
EllapsedTime: 96.0 seconds
RetCode: 0
Status:  OK 
CheckDir: KEGGgraph.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/KEGGgraph.Rcheck’
* using R version 2.14.2 (2012-02-29)
* 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 ‘1.10.0’
* 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 whether package ‘KEGGgraph’ can be installed ... OK
* checking installed package size ... 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... NOTE
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                             old_size new_size compress
  colorectalcancerSPIA.RData    955Kb    825Kb       xz
* 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 for unstated dependencies in vignettes ... NOTE
‘library’ or ‘require’ call not declared from: ‘RColorBrewer’
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

KEGGgraph.Rcheck/00install.out:

* installing *source* package ‘KEGGgraph’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘KEGGgraph.Rnw’ 
   ‘KEGGgraphApp.Rnw’ 
** testing if installed package can be loaded

* DONE (KEGGgraph)

KEGGgraph.Rcheck/KEGGgraph-Ex.timings:

nameusersystemelapsed
KEGGEdge-class0.9920.0161.029
KEGGEdgeSubType-class0.0000.0000.001
KEGGEdgeSubtype0.0080.0040.011
KEGGGraphics-class0.0000.0000.001
KEGGGroup-class0.0040.0000.001
KEGGNode-class0.5320.0000.541
KEGGPathway-class0.8240.0000.859
KEGGPathwayInfo-class0.4560.0040.460
KEGGReaction-class0.8240.0040.854
KEGGpathway2Graph0.5480.0000.548
KEGGpathway2reactionGraph0.8920.0000.895
expandKEGGPathway1.2880.0041.293
getDisplayName-methods0.4800.0040.482
getEntryID-methods0.5000.0000.501
getKEGGID-methods0.2720.0000.272
getKEGGgeneLink-methods0.0000.0040.000
getKEGGnodeData1.5040.0081.512
getKGMLurl0.0080.0201.069
getName-methods0.4400.0120.450
getNamedElement000
getPathwayInfo-methods0.4760.0080.483
getReactions-methods0.8000.0080.808
getRgraphvizEdgeNames0.0040.0000.003
getSubtype-methods0.5400.0040.541
getTitle-methods0.5120.0000.518
getType-methods0.9560.0040.963
graphDensity0.0040.0000.004
isHomoList0.0000.0000.001
mergeKEGGgraphs2.9490.0082.958
neighborhood0.2440.0040.248
parseKGML0.5880.0000.601
parseKGML2DataFrame2.1520.0042.217
parseKGML2Graph1.6920.0121.730
plotKEGGgraph2.9520.0042.957
pvalue2asterisk000
queryKEGGsubgraph1.5320.0041.536
randomSubGraph0.0320.0000.032
splitKEGGgroup0.5560.0000.558
subGraphByNodeType1.7280.0001.730
subKEGGgraph1.3400.0001.369
translateKEGGID2GeneID0.0000.0000.001
translateKEGGgraph1.9160.0121.996