* using log directory 'd:/Rcompile/CRANpkg/local/2.12/graphite.Rcheck'
* using R version 2.12.2 (2011-02-25)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* checking for file 'graphite/DESCRIPTION' ... OK
* this is package 'graphite' version '1.1'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'graphite' can be installed ... 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... WARNING
Warning in get_S4_generics_with_methods(code_env) :
  Generics g in env = <environment: namespace:graphite> where hasMethods(g, env) errors: 'edges', 'nodes'
May need something like

  importFrom("graph", "edges")
  importFrom("graph", "nodes")

in NAMESPACE.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... WARNING
Warning in get_S4_generics_with_methods(code_env) :
  Generics g in env = <environment: namespace:graphite> where hasMethods(g, env) errors: 'edges', 'nodes'
May need something like

  importFrom("graph", "edges")
  importFrom("graph", "nodes")

in NAMESPACE.
The argument of a replacement function which corresponds to the right
hand side must be named 'value'.
* checking foreign function calls ... WARNING
Warning in get_S4_generics_with_methods(code_env) :
  Generics g in env = <environment: namespace:graphite> where hasMethods(g, env) errors: 'edges', 'nodes'
May need something like

  importFrom("graph", "edges")
  importFrom("graph", "nodes")

in NAMESPACE.
See the chapter 'System and foreign language interfaces' of the
'Writing R Extensions' manual.
* checking R code for possible problems ... NOTE
Error in loadNamespace(i[[1L]], c(lib.loc, .libPaths())) : 
  there is no package called 'XMLRPC'
cytoscapePlot: no visible global function definition for
  'initEdgeAttribute'
cytoscapePlot: no visible global function definition for
  'CytoscapeConnection'
cytoscapePlot: no visible global function definition for
  'getWindowList'
cytoscapePlot: no visible global function definition for 'deleteWindow'
cytoscapePlot: no visible global function definition for
  'new.CytoscapeWindow'
cytoscapePlot: no visible global function definition for 'displayGraph'
cytoscapePlot: no visible global function definition for
  'setEdgeTargetArrowRule'
cytoscapePlot: no visible global function definition for 'redraw'
* 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 data for non-ASCII characters ... NOTE
  Note: found 8 marked UTF-8 string(s)
* checking examples ... ERROR
Running examples in 'graphite-Ex.R' failed
The error most likely occurred in:

> ### Name: runDEGraph
> ### Title: Run topological analysis on expression dataset using DEGraph
> ###   package. See 'testOneGraph'.
> ### Aliases: runDEGraph
> ### Keywords: topology analysis DEGraph
> 
> ### ** Examples
> 
> library(DEGraph)
Loading required package: R.utils
Loading required package: R.oo
Loading required package: R.methodsS3
R.methodsS3 v1.2.1 (2010-09-18) successfully loaded. See ?R.methodsS3 for help.
R.oo v1.8.2 (2011-08-25) successfully loaded. See ?R.oo for help.
R.utils v1.8.5 (2011-10-16) successfully loaded. See ?R.utils for help.
Scalable Robust Estimators with High Breakdown Point (version 1.3-01)
> data("Loi2008_DEGraphVignette")
> 
> p <- convertIdentifiers(biocarta[["actions of nitric oxide in the heart"]], "entrez")
> runDEGraph(p, exprLoi2008, classLoi2008)
Error in checkPkgVersion("DEGraph", "1.4.0") : 
  the installed DEGraph version is too old (need at least 1.4.0)
Calls: runDEGraph -> checkPkgVersion
Execution halted