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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: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch KEGGgraph_1.10.0.tar.gz
StartedAt: 2012-03-24 02:04:13 -0700 (Sat, 24 Mar 2012)
EndedAt: 2012-03-24 02:07:15 -0700 (Sat, 24 Mar 2012)
EllapsedTime: 181.7 seconds
RetCode: 0
Status:  OK 
CheckDir: KEGGgraph.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/KEGGgraph.Rcheck'
* using R version 2.14.2 (2012-02-29)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* 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 sizes of PDF files under 'inst/doc' ... 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 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-class1.2160.0221.381
KEGGEdgeSubType-class0.0010.0000.001
KEGGEdgeSubtype0.0130.0030.190
KEGGGraphics-class0.0000.0000.001
KEGGGroup-class0.0020.0010.002
KEGGNode-class0.6680.0080.753
KEGGPathway-class1.1190.0091.205
KEGGPathwayInfo-class0.6330.0060.691
KEGGReaction-class1.1340.0101.164
KEGGpathway2Graph0.7530.0090.811
KEGGpathway2reactionGraph1.1400.0081.177
expandKEGGPathway1.5920.0081.616
getDisplayName-methods0.7190.0040.823
getEntryID-methods0.6400.0050.676
getKEGGID-methods0.3250.0040.352
getKEGGgeneLink-methods0.0010.0000.001
getKEGGnodeData1.8730.0131.942
getKGMLurl0.0050.0130.179
getName-methods0.6500.0200.729
getNamedElement000
getPathwayInfo-methods0.6670.0060.697
getReactions-methods1.2440.0151.327
getRgraphvizEdgeNames0.0020.0000.003
getSubtype-methods0.6120.0050.645
getTitle-methods0.6450.0040.707
getType-methods1.0700.0061.128
graphDensity0.0040.0000.004
isHomoList0.0010.0000.001
mergeKEGGgraphs3.630.023.91
neighborhood0.3920.0301.057
parseKGML0.6570.0040.749
parseKGML2DataFrame3.1780.0153.270
parseKGML2Graph1.8480.0121.896
plotKEGGgraph 4.109 0.06810.286
pvalue2asterisk0.0010.0000.001
queryKEGGsubgraph2.0110.0132.141
randomSubGraph0.0400.0010.041
splitKEGGgroup0.7230.0040.736
subGraphByNodeType1.9100.0082.019
subKEGGgraph1.8680.0101.928
translateKEGGID2GeneID0.0010.0010.001
translateKEGGgraph2.0870.0132.300