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Package 297/553HostnameOS / ArchBUILDCHECKBUILD BIN
KEGGgraph 1.12.0
Jitao David Zhang
Snapshot Date: 2012-09-23 17:01:39 -0700 (Sun, 23 Sep 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/KEGGgraph
Last Changed Rev: 64678 / Revision: 69725
Last Changed Date: 2012-03-30 15:05:02 -0700 (Fri, 30 Mar 2012)
lamb2 Linux (openSUSE 11.4) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: KEGGgraph
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch KEGGgraph_1.12.0.tar.gz
StartedAt: 2012-09-24 00:42:35 -0700 (Mon, 24 Sep 2012)
EndedAt: 2012-09-24 00:44:42 -0700 (Mon, 24 Sep 2012)
EllapsedTime: 127.7 seconds
RetCode: 0
Status:  OK 
CheckDir: KEGGgraph.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.10-bioc/meat/KEGGgraph.Rcheck'
* using R version 2.15.1 (2012-06-22)
* 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 '1.12.0'
* 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 ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'kegg2graph.R'
  Running 'testGraph.R'
 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.10-bioc/meat/KEGGgraph.Rcheck/00check.log'
for details.

KEGGgraph.Rcheck/00install.out:

* installing *source* package 'KEGGgraph' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'KEGGgraph.Rnw' 
   'KEGGgraphApp.Rnw' 
** testing if installed package can be loaded

* DONE (KEGGgraph)

KEGGgraph.Rcheck/KEGGgraph-Ex.timings:

nameusersystemelapsed
KEGGEdge-class1.3980.0121.410
KEGGEdgeSubType-class0.0010.0000.001
KEGGEdgeSubtype0.0120.0030.014
KEGGGraphics-class0.0010.0010.001
KEGGGroup-class0.0010.0000.001
KEGGNode-class0.7790.0050.783
KEGGPathway-class1.3080.0081.316
KEGGPathwayInfo-class0.7260.0050.731
KEGGReaction-class1.2100.0061.216
KEGGpathway2Graph0.6930.0030.697
KEGGpathway2reactionGraph0.7800.0050.786
expandKEGGPathway1.5740.0051.579
getDisplayName-methods0.7830.0040.788
getEntryID-methods0.7650.0040.769
getKEGGID-methods0.4100.0030.412
getKEGGgeneLink-methods000
getKEGGnodeData2.3920.0062.399
getKGMLurl0.0050.0100.016
getName-methods0.7310.0260.757
getNamedElement0.0000.0000.001
getPathwayInfo-methods0.7160.0050.720
getReactions-methods1.2810.0071.287
getRgraphvizEdgeNames0.0030.0000.003
getSubtype-methods0.7930.0030.797
getTitle-methods0.6130.0040.617
getType-methods1.1560.0111.167
graphDensity0.0070.0000.007
isHomoList0.0010.0000.001
mergeKEGGgraphs3.0650.0113.080
neighborhood0.5900.0230.616
parseKGML0.7400.0040.745
parseKGML2DataFrame3.4790.0063.487
parseKGML2Graph2.1130.0072.122
plotKEGGgraph3.6020.0193.678
pvalue2asterisk0.0000.0010.001
queryKEGGsubgraph1.9960.0062.004
randomSubGraph0.0470.0000.047
splitKEGGgroup0.7750.0040.779
subGraphByNodeType1.5570.0051.563
subKEGGgraph1.5970.0051.602
translateKEGGID2GeneID0.0000.0000.001
translateKEGGgraph1.7010.0081.712