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Package 244/467HostnameOS / ArchBUILDCHECKBUILD BIN
KEGGgraph 1.8.0
Jitao David Zhang
Snapshot Date: 2011-10-20 07:20:33 -0700 (Thu, 20 Oct 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_8/madman/Rpacks/KEGGgraph
Last Changed Rev: 54800 / Revision: 59457
Last Changed Date: 2011-04-13 15:27:35 -0700 (Wed, 13 Apr 2011)
lamb1 Linux (openSUSE 11.3) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ WARNINGS ] OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  ERROR  OK 

Summary

Package: KEGGgraph
Version: 1.8.0
Command: D:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch KEGGgraph_1.8.0.tar.gz
StartedAt: 2011-10-20 15:00:45 -0700 (Thu, 20 Oct 2011)
EndedAt: 2011-10-20 15:02:24 -0700 (Thu, 20 Oct 2011)
EllapsedTime: 98.6 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: KEGGgraph.Rcheck
Warnings: 1

Command output

* using log directory 'D:/biocbld/bbs-2.8-bioc/meat/KEGGgraph.Rcheck'
* using R version 2.13.2 (2011-09-30)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'KEGGgraph/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'KEGGgraph' version '1.8.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... 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 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 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' ... WARNING
Package vignette(s) without corresponding PDF:
   KEGGgraph.Rnw
   KEGGgraphApp.Rnw

* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  'D:/biocbld/bbs-2.8-bioc/meat/KEGGgraph.Rcheck/00check.log'
for details

KEGGgraph.Rcheck/00install.out:

* installing *source* package 'KEGGgraph' ...
** R
** data
** inst
** preparing package for lazy loading
Warning in fun(...) :
  Rgraphviz built with Graphviz version 2.20.3.
Found installed Graphviz version 2.25.20090912.445. This _may_ cause problems.
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
Warning message:
In fun(...) : Rgraphviz built with Graphviz version 2.20.3.
Found installed Graphviz version 2.25.20090912.445. This _may_ cause problems.

* DONE (KEGGgraph)

KEGGgraph.Rcheck/KEGGgraph-Ex.timings:

nameusersystemelapsed
KEGGEdge-class1.30.01.3
KEGGEdgeSubType-class000
KEGGEdgeSubtype0.000.010.01
KEGGGraphics-class000
KEGGGroup-class000
KEGGNode-class0.720.000.72
KEGGPathway-class1.140.001.14
KEGGPathwayInfo-class0.590.000.60
KEGGReaction-class1.080.001.07
KEGGpathway2Graph0.770.020.79
KEGGpathway2reactionGraph1.040.011.06
expandKEGGPathway1.590.001.60
getDisplayName-methods0.640.000.64
getEntryID-methods0.600.000.59
getKEGGID-methods0.310.000.31
getKEGGgeneLink-methods000
getKEGGnodeData1.860.001.88
getKGMLurl000
getName-methods0.550.000.55
getNamedElement000
getPathwayInfo-methods0.580.000.58
getReactions-methods101
getRgraphvizEdgeNames0.020.000.01
getSubtype-methods0.670.000.67
getTitle-methods0.680.000.69
getType-methods1.210.001.20
graphDensity000
isHomoList000
mergeKEGGgraphs3.530.003.53
neighborhood0.040.000.03
parseKGML0.670.000.67
parseKGML2Graph1.900.001.91
plotKEGGgraph3.80.03.8
pvalue2asterisk000
queryKEGGsubgraph1.860.001.86
randomSubGraph0.030.000.03
splitKEGGgroup0.660.000.65
subGraphByNodeType1.940.001.94
subKEGGgraph1.810.001.81
translateKEGGID2GeneID000
translateKEGGgraph1.750.001.75