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Package 327/609HostnameOS / ArchBUILDCHECKBUILD BIN
KEGGgraph 1.14.0
Jitao David Zhang
Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/KEGGgraph
Last Changed Rev: 70050 / Revision: 74773
Last Changed Date: 2012-10-01 15:16:24 -0700 (Mon, 01 Oct 2012)
lamb1 Linux (openSUSE 12.1) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: KEGGgraph
Version: 1.14.0
Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings KEGGgraph_1.14.0.tar.gz
StartedAt: 2013-03-25 02:33:05 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 02:35:03 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 118.6 seconds
RetCode: 0
Status:  OK 
CheckDir: KEGGgraph.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/KEGGgraph.Rcheck’
* using R version 2.15.3 (2013-03-01)
* 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 ‘1.14.0’
* 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 for left-over 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 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
  ‘/loc/home/biocbuild/bbs-2.11-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-class0.9560.0120.977
KEGGEdgeSubType-class0.0000.0000.001
KEGGEdgeSubtype0.0120.0000.010
KEGGGraphics-class0.0000.0000.001
KEGGGroup-class000
KEGGNode-class0.5920.0000.596
KEGGPathway-class0.8440.0000.846
KEGGPathwayInfo-class0.5840.0000.581
KEGGReaction-class0.9040.0040.908
KEGGpathway2Graph0.6400.0000.637
KEGGpathway2reactionGraph0.9400.0000.942
expandKEGGPathway1.4840.0001.486
getDisplayName-methods0.4920.0080.501
getEntryID-methods0.5120.0000.509
getKEGGID-methods0.260.000.26
getKEGGgeneLink-methods0.0000.0000.001
getKEGGnodeData1.6520.0041.745
getKGMLurl0.0080.0241.733
getName-methods0.6240.0160.692
getNamedElement0.0000.0000.001
getPathwayInfo-methods0.5600.0000.581
getReactions-methods0.8400.0000.844
getRgraphvizEdgeNames0.0040.0000.003
getSubtype-methods0.4960.0040.497
getTitle-methods0.5560.0080.567
getType-methods0.9680.0000.972
graphDensity0.0040.0000.004
isHomoList0.0000.0000.001
mergeKEGGgraphs3.1970.0043.279
neighborhood0.2640.0080.276
parseKGML0.6440.0040.646
parseKGML2DataFrame2.3240.0082.333
parseKGML2Graph1.8720.0001.877
plotKEGGgraph3.1360.0163.155
pvalue2asterisk0.0040.0000.001
queryKEGGsubgraph1.5840.0001.584
randomSubGraph0.0320.0000.030
splitKEGGgroup0.5920.0000.593
subGraphByNodeType1.6520.0041.658
subKEGGgraph1.7730.0001.897
translateKEGGID2GeneID000
translateKEGGgraph1.9200.0041.970